diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 00000000..d489d694 --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,23 @@ +version: 2 +jobs: + build: + docker: + - image: circleci/python:2.7.15-stretch-node + steps: + - checkout + - run: + name: setup environment + command: | + mkdir ~/env + virtualenv ~/env + source ~/env/bin/activate + pip install -r requirements_dev.txt + pip install -r requirements.txt + - run: + name: running tests + command: | + mkdir ~/test_reports + source ~/env/bin/activate + pytest --junitxml=~/test_reports/pytest-results.xml + - store_test_results: + path: ~/test_reports diff --git a/.gitignore b/.gitignore index b9dbb304..b927b68e 100644 --- a/.gitignore +++ b/.gitignore @@ -45,6 +45,7 @@ nosetests.xml coverage.xml *.cover .hypothesis/ +.pytest_cache/ # Translations *.mo @@ -102,3 +103,7 @@ ENV/ # Pycharm .idea + +# intermediate test data +tests/data/genome/ +/scripts/generate_gt_file.py diff --git a/README.md b/README.md new file mode 100644 index 00000000..a9ace880 --- /dev/null +++ b/README.md @@ -0,0 +1,435 @@ +# immuno +immuno is a script which predicts the pepetide sequency from the RNA sequency splicegraph. You can specify the donor and output using the command line below. + + +``` +python main_immuno.py --donor TCGA-13-1489 --output_dir test --splice_path quick_test_data/sample_gene.pkl --ann_path quick_test_data/small.gtf --ref_path quick_test_data/smallgene34.fa +python exon_filter.py --meta_file test/TCGA-13-1489/ref_meta1.tsv.gz --peptide_file test/TCGA-13-1489/ref_peptide2.fa +``` + +If you add the expression information, make sure there are `.merge_graphs.pickle` and `.merge_graphs.count.hdf5` files in the same folder. +The github repo provides the splicegraph `sample_gene.pkl` and the annotation information `small.gtf` +but not with the genome sequence `smallgene34.fa` because it is too large. + +You should download the genome from other places. We are using the `hg19_hs37d5` version for testing. + +### Immunopepper Installation + +It is recommended to setup a separate virtual or conda environment. + +The basic immunopepper package can be installed from source using: +``` +pip install -r requirements.txt -r requirements_dev.txt +make install +``` + +After that, consult the output of the following command for usage options +``` +immunopepper -h +``` + +### update 14/09/2018 +1. To avoid multimapper case, which might obscure our estimate for the expression count data, the test case +is splitted into positive and negative case. In the following development, all the test case will also +consists two parts. + +2. Change the hierarchy of test directory. In future development, we just need create new test case `test2`, `test3`. More pre +cisely, creating `test2pos.fa`, `test2pos.maf`, `test2pos.vcf`, `test2pos.gtf`. Then run `create_bam_file` to generate the corresponding negative case +Follow the next steps stated in `step.sh`. The groundtruth file can be generated automatically in `tests/test2/test2pos` or `tests/test2/test2neg`. Make some +small changes on the `test_end_to_end.py` file. The whole process is done. + +> + + . + ├── ... + ├── tests # root directory for all tests + │ ├── test1 + │ ├── test2 + │ └── test3 + │ ├── test3pos # groundtruth for positive case + │ ├── test3neg # groundtruth for negative case + │ └── data # test data for test3 + │ + │ # Unit tests + └── ... + +3. Move scripts to `./scripts` directory and keep the `./immunopepper` a real packaeg. +4. Calculate all the theoretical value for segment expression in `scripts/validate_count.py`. +5. are incorrect in total 12 segments. Need further check. + +##### Future work +Some bash script trick. How to make the `test1`, `test2` flexible variable? like `'insert_a_variable{}'.format('_with_format')` + +### update 10/09/2018 +1. Add a copy dictionary of `gene.reading_frames` in `immuno_model.py`. Avoid dynamic changes of `gene` object. +2. Add a `constant.py` file and create an important global variable `NOT_EXIST`. It will appear in many places including +**isolated exon case**, **no mutastion exist case** etc. +3. Decapitalize the namedtuple name. + + +### update 07/09/2018 +1. Split the computation and writing parts of `annotate_gene_opt`. Because of this modification, we can +filter the redundant peptide completely accurate. see `18/06/2018` for more details +2. Use namedtuple to improve the readability of functions. +3. Achieve two new features: + * calculate the mean segment expression counts. Instead of only replying on the junction expression counts, + we add one more data to support the expression level of the given exon pair. + * Generate the libsize level file. + +##### Future work +1. Still have some questions about the count file. + * The count data in the current test case might be inaccurate. + * why the `strain_id` in `count.h5` file is `Aligned.sortedByCoord.out`, how to change it? + * How to include more count data in one `count.h5` file? +2. Better to test on the big data to see if something important is ommitted. + +### update 24/08/2018 +1. Add new test cases. There are 7 transcripts, 7 vertices and 13 output pairs in total in the new test cases. Tests include + * read_frame propogation + * somatic and germline mutation + * filter function + * isolated exon case +2. When running the test case, fix some bugs: + * `is_output_redundant`. The current function in `master` branch is wrong because it does not consider the read_frame compare. + * `get_sub_mut_seq`. Will cause bug when the mutation position is on the boundary. The original one in `master` will cause bug because sometimes the `start_v1` is not + eqal to the the start position of exon due to read_frame shift. + * `isolated_peptide_result`. In the negative strand case, the reference should be transformed using `complementary_seq`. +3. Refine the whole process for test case creation in `step.sh` +Put all the steps in the `step.sh` so that it will be quicker to change the test case case in the future. + +##### Future work +1. Refactor the code. + * Split the `immuno_model.py` into two parts for computation and writing. Making the loop of body another function. + * Using named tuple to avoid complex return value + * Find a way to avoid making changes on the gene object. +2. Merge into the `fix/envCleanup` branch. +3. Achieve new requirement on the k-mer expression data. + + +### update 13/08/2018 +1. Build the basic test pipline using `pytest` module. It consists of two parts: test for one of the core function `get_sub_mut_dna` and test for all the output file (`peptide.fa`, `metadata.tsv`) in four modes (`ref`, `germline`, `somatic`, `somatic_and_germline`). Type the following command for testing. Remember to include `modules` directory from `spladder` repo in the work directory. +``` +python -m pytest test_immunopepper.py +``` +2. Generate artifical expression data and corresponding splicegraph count file. The steps are recored in `step.sh` file. + +3. Update the test file after including the count file and fix one small bug. + + +##### Future work +1. More test case for other core functions which may change in the following versions. For example `cross_peptide_result` +2. The artificial `count file` is a little bit different from what was given in the past. Need further confirmation and change if we want to test or use the count file.In the `.count.hdf5`, the `strains` attribute is `Aligned.sortedByCoord.out` instead of `test1`. `gene_names` atrribute shape is (2,1) instead of (2,) so that an additional Index is needed, which is not the case for the previous example file. (See the details In the `parse_gene_metadata_info` function in `immuno_preprocess` module, line 209-211, line 225 and line 231). +3. Need to deal well with `modules` from `spladder` repo. It's a little annoying. + +### update 31/07/2018 +1. Add the unittest file `test1.fa`, `test1.vcf`, `test1.maf` and the corresponding splicegraph. +Add the function that generates the test file to the `utils` module. That is `create_test_genome` +and `create_full_from_pos` + +2. Fix some bugs in different mutation mode after tested on the test file: + * fix the `sub_dna` creation problem in negative strand case in `get_sub_mut_dna` file. + * fix the output problem in `germline` mode (which is supposed to output the peptide that not exists in the reference sequence) + +##### Future work +1. Create the `.bam` file and based on that create the `.hdf5` encoding the expression information +2. Read relative contents on `pytest`. Combine the current test case with standard python test framework. + +### update 21/07/2018 +Improve the the speed of mutation mode implementation. In the version before, `mut_seq_dict` +is created, with keys the variant position and values the whole genome sequence. It is a huge waste +because the these different sequences only different in very limited part (just 2 or 3 positions but +we need copy and create new string of about length of over 100 million) + +Therefore, instead of copying and pasting the whole genome sequence, we just create a +very small subset of dna string (the range which cover the junction pair). It dramatically +decreases the implementation time. + +### update 18/07/2018 +1. Add two flags `has_stop_codon` and `is_in_junction_list`. The first new flag indicates if the +output peptide contain stop codon. The underscore `_` symnol is removed in the final output +since the new flag already contains the necessary information. The second new flag is +another way of filtering. From the comparison between the normal sample and cancer sample, we know some +exon pairs exist in gene of both type (normal or cancer) and thus those exon pairs +are less likely to be the key pairs. The new flag is based on the externel file `gtex_junctions.hdf5` + +2. Fix a bug caused by different notations. Now all the non-existing value is `.` ( + * the `variant_comb` is `.` if no variant exist in the exon pair; + * the `seg_expr` and `junction_expr` is `.` if no count info is provided + * the `junction_annotated` and `is_in_junction_list` is `.` if it is an isolated exon + +3. Rearrange the output column. Now all the 5 flags are in the same part. + +##### Future work +1. Wait for the suggestion when used in the real application. +2. Need improvement when used in mutation mode. It's both time and memory consuming. + +### update 30/06/2018 +1. Found some assertion fail. + * The `cds_stop` does not equal to the `v_stop` (if `strand == -` + )or `cds_stop` does not equal to the `v_start` (if `strand == +`). Which + validate further the necessaty of having the reading frame tuple `(cds_start, cds_stop, read_frame)` + instead of only `read_frame` + * The isolated cds may not contain stop codon. Which is contrary to our + basic assumption. + +A good example may be the `No.14` (0-based) gene in `splicegraph`. Focus on +the `No.70` vertex. The coordinate is `(50211225,50211389)`. From the corresponding `.gtf` file, +we know there is a cds within that region, with +``` +3 HAVANA CDS 50211318 50211386 . + 0 gene_id "ENSG00000001617.7"; transcript_id "ENST00000413852.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "SEMA3F"; transcript_type "protein_coding"; transcript_status "NOVEL"; transcript_name "SEMA3F-004"; exon_number 3; exon_id "ENSE00003521450.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000156806.7"; havana_transcript "OTTHUMT00000345962.1"; +``` +. It's obvious that it that `50211386` does not equal to `50211389` + +Also, the `No.70` vertex has no successive vertice. But it got two read frames. +The above line is one of the read frames.We have +``` +seq_dict['3'][50211317:50211386] = ATGTACGTGGGCAGCAAGGACTACGTGCTGTCCCTGGACCTGCACGACATCAACCGCGAGCCCCTCATT +``` +The translated peptide is `MYVGSKDYVLSLDLHDINREPLI`, no stop codon. + +2. Questions about the new splicegraph. I found the new version splicegraph is different from +the previous one. The most obvious change is the number of vertices: the former splicegraph +has usually around 10 vertices which the new version has more than 400. Quite a lot of +vertices are in overlap. For example, `No.58`, `No.59`, `No.60`, `No.61`, all of those are +connected with `No.70`. The coordinates for the four vertices are +`(5029054,5029254), (50209124, 50209324), (50209426,50209626), (50209485,50209626)`. You can see +they have some overlappings. `No.67`, `No.68`, `No.69` and `No.70` also very close (share the beginning). +The coordinates are `(50211225,50211259), (_,50211319), (_,50211386), (_,50211389)` + +The question is, do we need so many overlapping vertices? + +3. Fix the small bug for `exon_filter.py`. Since there are a lot of overlapping vertices +in the new splicegraph. The `exon_filter.py` is more important, which can filter over `40%` +of the peptide. The inner filter module `is_redundant` will not be so useful on this case because most +vertices are in ascending order and as we claim before, in this case, the formal one is redundant but +since it is already written in file so it will not be filtered. + +4. Write two logging file `cds_match_log.txt` (`gene_id \t vertex_id` each line)and `isolated_stop` (`gene_name \t vertex_id` each line) + +### Update 22/06/18 +1. Fix the bug of coordinate mismatch between gene (1-based) and +python (0-based). Now the output peptide on the testset is right. + +2. Finalize the filter part on the new structure. Now two ways of +filtering are provided. There is a filter function embedded in `annotate_gene_opt`, +which is `is_output_redundant`. However, since for each output, it +can only be compared with the past output. So there might be some +false negative (the redundant output which should be filtered) +The external way of filtering is the `exon_filter`. Since the global +picture can be seen, the result is 100 percent correct. The reason +why not put the `exon_filter` into `annotate_gene_opt` is that it will +make the code fat (every line of output should be stored). Might +find a better solution in the future. + +##### Future work +1. Validate. The previous result can no longer be seen as the fully `ground_truth` +but partly true because there are some missing output. But all the output in the +previous code should also be present in the new output (with a little modification. eg. +stop outputting when meeting with the stop codon). Should find a +better way to validate the current code. + +2. Modify the mutation part. The code is right. But each time when +creating new mutated sequence in `apply_somatic_mutation`, a new +sequence string should be created, although just few of them are different, +which means we have huge redundance here. Need to be improved in the future. + +### Update 18/06/18 +1. Found a small bug in previous code: in the previous code, it is assumed that +the cds always starts at the beginning of vertices (that is `c1=v1` and `c2=v2`), +which actually is not. +2. According to the new requirement, the peptide which contain `stop_codon` should also be outputted until it reaches stop codon. +3. The vertice which has no connection with other vertices but has a cds, called `isolated cds`, should also +be outputted. + +Based on the two require, some relative big changes are made on the code. + +1. Rewrite the `read_frame` part. In the previous code, the `read_frame` is just the number of bases +that are left to the next vertices. In the new version, the `read_frame` is a tuple +of `(cds_begin_coord, cds_stop_coord,read_frame)`. The first two elements +marks the coding region in the given vertices. +2. Rewrite the vertice pair traverse. First, go through the sorted vertex (ascend if `strand == +` else descend) +If there is a read_frame in that vertex, go to the next inner loop, otherwise read next vertex. +3. Check if the vertex has neighbour, it yes, jump into `cross_peptide_result`. +If there is no stop codon, output the whole peptide result and propagate the `read_frame` to the next vertice. +If there is a stop codon within the vertice pair, output the peptide until it reaches the stop codon. The `read_frame` would +not be propagated. If the stop codon appear at the first vertice (which means no peptide from the second +vertice is outputted), set the flag `is_isolated` to be `True` +4. If the vertex has no neighbor but there is a `cds` in that vertex, it is an `isolated cds`. +The tranlated peptide would also be outputted. `is_isolated = True`, no `read_frame` will be propagated. + +##### Future work +1. The result should be validated. When tested on small data, the two tested gene just +output one line of peptide (which means they stop translating at the beginning of coding regions in +reference sequence, which is unbelievable). So far I didn't find the reason. + +2. Add the filter part. In the last commit, a filter module was added. Since the +loop was already quite different, a new compatible filter module should be designed. +Can also use `exon_filter_dict`.Or, we can just filter the output based on the +`start_v1/v2, stop_v1/v2`, the four numbers contain all the information needed to output the peptide result. + +### Update 12/06/18 +1. Validate the exon filter function, add the argument `is_filter` to the interface. When `is_filter` is set to `1`. The exon pair which is the subset of another exon pair will not be processes and the corresponsing peptide will not be output +2. Build two dictionary for comparing the ground truth output and the current output. + +##### Future work +1. Dealing with the `stop codon`. For now the exon pair with `stop codon` will not be translated and outputted, which is not enough for our future analysis. +2. Keep validating. + +### Update 28/05/18 +1. Add the case where no count file is provided (reference), add new argument `process_num`, which specifies how many genes to be processes in the splicegraph. Default is to process all genes +2. Write bash scripts to generate mini version of vcf and maf file for the future quick validation +3. Keep validating. + +### Update 27/05/18 +Finish the whole structure. +Below is the flowchar for the core module **annotate\_gene_opt**. + +1. Apply mutation information + + * If **.vcf** file is provided, the germline mutation will be encoded. If only **.vcf** is provided (mutation mode: `germline`), the output peptide will be those that are different from the original reference gene. + * If **.maf** file is provided, the somatic mutation will be encoded. Two dict are created (``som_expr_dict``, ``exon_som_dict``). The first one is used for output the expression info of the segment where the given somatic mutaiton is. The second is used for creating all the variant combination within the given exon pairs. + * For the `ref` mode, the original peptides are outputted. For the `germline` mode, the peptide which is different from the original peptides are outputted. For the `somatic` mode, the reference sequence is taken as the background sequence and any mutations causing different peptide are outputted. For the `somatic_and_germline` mode. The germline-mutated sequence is taken as the background sequnce. + +2. Build two flags for future filtering. + * flag0: Indicate if the given peptide output also exist in the expected pepide transcript given by annotation **.gtf** file. + * flag1: indicate if the junction pair also exist in annotation **.gtf** file +3. Add read phase for each exons +4. loop over each exon pair. Get all variant combnation within the pairs. If any exon combination exists, get the corresponding mutated sequence `mut_seq_dict`. +5. loop over different exon combination and read frames. +6. If the exon pair has no stop codon within the exon pair and the ref_gene is different from mut_gene, or just simplily in `ref` mode. Write the result line on the result file. + +The arguments in test. + +I try to find the common `donor` in **.h5** and **.maf** file, but failed. So I take the first two donor implied by the **pancan.merged.v0.2.6.PUBLIC.maf** and reduce to a small **.maf** file **mini2.maf** with the mutations that only belong to the two and create a new file **mini_count.h5**which the `strain` are also the two donor (which is actually not). I also only test two genes of over 20,000 genes in the splicegraph. + + +The complete argument table is shown below. + +| Args | input | +|---|---| +|-donor|TCGA-13-1489| +|-output_dir|test| +|-splice_path| ../evaluation\_data\_graph/genes\_graph\_conf3.merge_graphs.validated.pickle | +|-ann_path|/cluster/project/raetsch/lab/03/phrt_immuno/annotation/gencode.v19.annotation.hs37d5\_chr.spladder.gtf| +|-ref_path|../genome/hg19_hs37d5/genome.fa| +|-count_path|../evaluation_data/graph_metadata/genes_graph_conf3.merge_graphs.validated.count.h5| +|-maf|mini.maf| +|-vcf|mini_vcf.h5| + +##### Some statistics +1. loading the whole **count.h5** file is time-consuming, around `400` seconds on average. Loading the graph and preprocess the splicegraph are also time-consuming, around `200s` for each. Loading the whole **.maf** file is even much more time-consuming. So two mini-versioned count and maf file are created. +2. It also need a lot of memory. Usually I 8 CPU(1024 Mb memory for each )to load all these data when submmiting the work via bsub. Four CPUs are not enough. +3. If in `ref` mode, processing each gene costs less than 0.1 seconds. +but for the `somatic` mode, it takes much more time. (from 20s to 80s). Need further analysis to see where the time is spent. + +##### Need help +Find real matched **.h5** and **.maf**, **.vcf** file so that I can see how it is real going with the mutation part (currently since no mutation lies within any exon pair, the program never goes into that branch) + +##### Future work +1. Tested on more proper dataset +2. Future possible optimization +3. Add more processing message (like some error messages).Currently there is some assumption on the input. Eg. must provide the count file. + +### update 05/05/2018 +1. Refactor the code so it can be used in four scenarios:`ref`, `germline`, `somatic` and `somatic_and_germline` + + * `ref`: Ouput the peptide on the given splicegraph and reference gene. + * `germline`: code the germline variant info from **.vcf** file and only + output the peptide which is different from `ref` + * `somatic`: code the somatic variants info from **.maf** file and only + output the peptide which is different from `ref` + * `somatic_and_germline`: encode the variants info from both **.vcf** file nad **.maf** file. + using the germline-encoded sequence as the background seq. Only output + the peptide which is different from what are outputed from background seq. +2. Design a very simple test case: 2 variants in **.maf** and 2 +in **.vcf** +3. Create a new immuno module named `immuno_module` which include the core +function `annotate_gene_opt`. It is because we may need do a lot of complicated +loop/if-else control in the future (like dealing with deletion/insertion) +It's better to have a seperate file for the core module. + +The code has passed my two self-designed variant file on all four +scenarios. + +##### Future work +1. Apply on the real data and improve +2. Might be optimized in terms of speed and memory consumption +3. Deal with more complicated cases (deletion and insertion) + +### update 23/04/2018 +1. Ouput the junction expression data, which is in the **count.hdf5** and modified by the coefficient in the **lib_size** data +2. Remove some unnecessary argument. Eg. cluster option and load_expression_data. +3. Remove the **get_cfg** module and leave that part directly in the main part. + + +##### Future work +1. Create new flag based on the expression data +2. Clarify the input data format and keep refactor. + +### update 16/04/2018 +#### results + + +1. modularize the code.The details for all modules are shown below: + * **immuno_preprocess.py'**: include all the preprocess functions (eg: splicegraph, +annotation file, reference gene file). + * **immuno_filter.py**: include the flags for peptide filtering. Currently two flags. + * **immuno_mutation.py**: include the function dealing with mutation gene process (to be modified in the future). + * **inmuno_print.py**: all the print functions might be needed in the project. + * **utils.py**: all the auxiliary functions needed for output peptides (eg: dna translate, complementary seq) + * **main_immuno.py**: main functions. Dealing with the input parsing, iterating on the splicegene and call the core function **ann\_gene\_opt**. + * **get_cfg.py**: parsing the command line input and get the configuration parameters. + +2. add more arguments to the main file: + + * **-ann_path**, **splice_path**, **ref_path**. The three arguments can be used to specify the path of the needed input (might have **metagraph_path** in the future). All the path are regarded as the subdirectory of **work_dir**. + * **-load\_expression_data**. Currently not used in the main function because all the expression annotation data are commented. But it will be used in the future. + * **quick_test**. Since running on the whole dataset is time-consuming. Quick test mode can help quick validate the code. + * **cluster_option**. This code will usually run on two different clusters, which result two slightly different settings. Use this option to specify which option **[G/J]**. It will free us from change the code. + + +##### Future work +1. Start combine the expression data and mutation data in the flags. +2. Keep modularizing.Put all the parameter in the `args`. + +### update 08/04/2018 +##### results + +1. output 3 files. + * **meta.tsv**: the meta data of output like the gene name, two flags, etc. + * **peptide.fa**: the output peptide. + * **no\_output_gene.txt**: record all the genes that are not outputed at all(eg: contain stop codon at very beginning exons) +2. build 2 flags. + * **flag_background**: indicate whether the output peptide appear in the background peptide. + * **flag_cds**: indicate whether the exon pair also appear in the cds_list given by *.gtf* annotation file. +3. create **output_id**: the id looks like **gene_id**.**output_id**. There usually are more than one exon pairs in a gene, so we usually have **0.1**, **4.2**, **108.12**, etc + +##### future work +1. consider rare case where the single exon is ignored. +2. modularize the mode. + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/immunopepper/__init__.py b/immunopepper/__init__.py index e69de29b..0eedec29 100644 --- a/immunopepper/__init__.py +++ b/immunopepper/__init__.py @@ -0,0 +1,5 @@ +"""Top-level package for ratschlab common.""" + +__author__ = """Ratschlab""" +__email__ = 'andre.kahles@inf.ethz.ch' +__version__ = '1.0.0' diff --git a/immunopepper/constant.py b/immunopepper/constant.py new file mode 100644 index 00000000..2ed7ab07 --- /dev/null +++ b/immunopepper/constant.py @@ -0,0 +1,13 @@ +''' +In some cases, the output does not exist. So a special character is used in the output file. +Mainly on the flag field and expression counts field in the output .tsv file +For example, + +- flag field IS_IN_JUNCTION_LIST if no external junction file is provided +- flag field JUNCTION_ANNOTATED if it is an isolated exon +- field VARIANT_COMBINE if no variant existing in the exon-pair +- expression field VARIANT_SEG_EXPR if no variant existing in the exon-pair +- expression field JUNCTION_EXPR if it is an isolated exon +''' + +NOT_EXIST = '.' diff --git a/immunopepper/exon_filter.py b/immunopepper/exon_filter.py deleted file mode 100644 index 9b683930..00000000 --- a/immunopepper/exon_filter.py +++ /dev/null @@ -1,98 +0,0 @@ -import argparse -import gzip -import re - -def get_exon_dict(meta_file_path): - if meta_file_path.endswith('gz'): - f = gzip.open(meta_file_path, 'r') - else: - f = open(meta_file_path, 'r') - exon_dict = {} - for line in f: - ### handle header - if line.startswith('output_id'): - header = line.strip().split('\t') - eidx = header.index('exons_coor') - continue - items = line.strip().split('\t') - exon_list = items[eidx].split(';') - idx = items[0] - gene_name = items[2] - strand = items[4] - if strand == '+': - key = (gene_name, exon_list[1],exon_list[2]) - if key in exon_dict: - exon_dict[key].append((idx,exon_list[0],exon_list[3])) - else: - exon_dict[key] = [(idx,exon_list[0],exon_list[3])] - else: - key = (gene_name, exon_list[0], exon_list[3]) - if key in exon_dict: - exon_dict[key].append((idx, exon_list[2], exon_list[1])) - else: - exon_dict[key] = [(idx, exon_list[2], exon_list[1])] - return exon_dict - -def get_remove_id(exon_dict): - remove_id_list = [] - for exon_pair_list in exon_dict.values(): - L = len(exon_pair_list) - if L < 2: - continue - for i, exon_pair in enumerate(exon_pair_list): - for j in range(L): - i_pos1 = exon_pair[1] - i_pos2 = exon_pair[2] - j_pos1 = exon_pair_list[j][1] - j_pos2 = exon_pair_list[j][2] - if j!=i and i_pos1 >= j_pos1 and i_pos2 <= j_pos2: - if exon_pair[0] == '33803.7': - print exon_pair_list - remove_id_list.append(exon_pair[0]) - break - return remove_id_list - - -def get_filtered_output(meta_file, peptide_file, remove_id_list): - if meta_file.endswith('gz'): - fin1 = gzip.open(meta_file, 'r') - fout1 = gzip.open(re.sub(r'.tsv.gz$', '', meta_file) + '.filt.tsv.gz', 'w') - else: - fin1 = open(meta_file, 'r') - fout1 = open(re.sub(r'.tsv$', '', meta_file) + '.filt.tsv', 'w') - fin2 = open(peptide_file) - fout2 = open(re.sub(r'.fa$', '', peptide_file) + '.filt.fa', 'w') - header_line = fin1.readline() - fout1.write(header_line) - lines1 = fin1.readlines() - lines2 = fin2.readlines() - for i,line in enumerate(lines1): - items = line.strip().split('\t') - if items[0] not in remove_id_list: - print(items[0]) - fout1.write(line) - fout2.write(lines2[2*i]) - fout2.write(lines2[2*i+1]) - fin1.close() - fin2.close() - fout1.close() - fout2.close() - -if "__name__" is not "__main__": - parser = argparse.ArgumentParser() - parser.add_argument("--meta_file", nargs=1, help="the generated meta tsv file name", required=True) - parser.add_argument("--peptide_file", nargs=1, help="the corresponding peptide file", required=True) - args = parser.parse_args() - meta_file = args.meta_file[0] - peptide_file = args.peptide_file[0] - # meta_file = 't/TCGA-13-1489/ref_meta1.tsv.gz' - # peptide_file = 't/TCGA-13-1489/ref_peptide2.fa' - exon_dict = get_exon_dict(meta_file) - remove_id_list = get_remove_id(exon_dict) - get_filtered_output(meta_file, peptide_file, remove_id_list) - - - - - - diff --git a/immunopepper/immuno_filter.py b/immunopepper/immuno_filter.py index 22712e6c..3e771422 100644 --- a/immunopepper/immuno_filter.py +++ b/immunopepper/immuno_filter.py @@ -1,13 +1,28 @@ +"""Contain the function used for filtering""" import sys import re -# external package import scipy as sp -# immuno module from utils import complementary_seq,translate_dna_to_peptide + def junction_is_annotated(gene, gene_to_transcript_table, transcript_to_cds_table): + """ Indicate whether exon pair also appears in transcript given by .gtf file + + Parameters + ---------- + gene: Object. Created by SplAdder. + gene_to_transcript_table: Dict. "Gene" -> "transcript" + transcript_to_cds_table: Dict. "transcript" -> "cds" + + Returns + ------- + junction_flag: 2D array matrix with shape len(edges)*len(edges). + True indicates the exon pair also appear in gtf file + while False indicates the exon pair not exist or it does not show in the + given .gtf file. + """ ts_list = gene_to_transcript_table[gene.name] vertices = gene.splicegraph.vertices edges = gene.splicegraph.edges @@ -31,7 +46,90 @@ def junction_is_annotated(gene, gene_to_transcript_table, transcript_to_cds_tabl return junction_flag + +def find_background_transcript(gene, ref_seq, gene_to_transcript_table, transcript_cds_table): + """Calculate the transcript derived from the annotation file. + It is used for generating artificial reads. + + Parameters + ---------- + gene: Object. Created by SplAdder + ref_seq: List(str). Reference sequence of certain chromosome. + gene_to_transcript_table: Dict. "Gene" -> "transcript" + transcript_to_cds_table: Dict. "transcript" -> "cds" + + Returns + ------- + ts_list: List[str]. List of all the peptide translated from the given + splicegraph and annotation. + """ + gene_transcripts = gene_to_transcript_table[gene.name] + ts_list = [] + + # Generate a background peptide for every variant transcript + for ts in gene_transcripts: + + # No CDS entries for transcript in annotation file... + if ts not in transcript_cds_table: + # print("WARNING: Transcript not in CDS table") + continue + + cds_list = transcript_cds_table[ts] + + # Reverse CDS in reverse strand transcription... + # add 3 bases to the last cds part to account for non-annotated stops + if gene.strand.strip() == "-": + cds_list = cds_list[::-1] + cds_list[-1] = (cds_list[-1][0] - 3, cds_list[-1][1], cds_list[-1][2]) + else: + cds_list[-1] = (cds_list[-1][0], cds_list[-1][1] + 3, cds_list[-1][2]) + + cds_string = "" + first_cds = True + + # Append transcribed CDS regions to the output + for coord_left, coord_right, frameshift in cds_list: + + # Apply initial frameshift on the first CDS of the transcript + if first_cds: + if gene.strand.strip() == "+": + coord_left += frameshift + else: + coord_right -= frameshift + first_cds = False + + nuc_seq = ref_seq[coord_left:coord_right + 1] + + # Accumulate new DNA sequence... + if gene.strand.strip() == "+": + cds_string += nuc_seq + elif gene.strand.strip() == "-": + cds_string += complementary_seq(nuc_seq[::-1]) + else: + print("ERROR: Invalid strand...") + sys.exit(1) + ts_list.append(cds_string) + #aa_str_mutated = translate_dna_to_peptide(cds_string) + #peptide_list.append((aa_str_mutated, ts)) + gene.processed = True + return ts_list + + def find_background_peptides(gene, ref_seq, gene_to_transcript_table, transcript_cds_table): + """Calculate the peptide translated from the complete transcript instead of single exon pairs + + Parameters + ---------- + gene: Object. Created by SplAdder + ref_seq: List(str). Reference sequence of certain chromosome. + gene_to_transcript_table: Dict. "Gene" -> "transcript" + transcript_to_cds_table: Dict. "transcript" -> "cds" + + Returns + ------- + peptide_list: List[str]. List of all the peptide translated from the given + splicegraph and annotation. + """ gene_transcripts = gene_to_transcript_table[gene.name] peptide_list = [] @@ -66,7 +164,7 @@ def find_background_peptides(gene, ref_seq, gene_to_transcript_table, transcript else: coord_right -= frameshift first_cds = False - + nuc_seq = ref_seq[coord_left:coord_right+1] # Accumulate new DNA sequence... @@ -85,6 +183,17 @@ def find_background_peptides(gene, ref_seq, gene_to_transcript_table, transcript def peptide_match(ref_peptides, peptide): + """ Find if the translated exon-pair peptide also appear in the annotation file. + + Parameters + ---------- + background_peptide_list: List(str) All the peptide translated from transcripts in annotation file + peptide: str. peptide translated from certain exon-pairs + + Returns + ------- + count: int. Count how many matches exist between background peptide and given peptide + """ match_ts_list = [] for ref in ref_peptides: ref_peptide = ref[0][0] @@ -93,37 +202,85 @@ def peptide_match(ref_peptides, peptide): match_ts_list.append(transcript) return match_ts_list -## Returns true if there is a stop codon in the sequence. All codons that are fully in the -# interval [start_coord<->end_coord] are checked. -# seq: Nucleotide sequence of vertex/CDS region -# start_coord: Read start coordinate -# stop_coord: Read stop coordinate -# strand: Read direction, one of {"+","-"} -def has_stop_codon_initial(seq, start_coord, end_coord, strand): - if strand == "+": - assert (start_coord <= end_coord) - substr = seq[start_coord - 1:end_coord] - else: # strand=="-" - assert (start_coord >= end_coord) - substr = complementary_seq(seq[end_coord - 1:start_coord][::-1]) - for idx in range(0, len(substr) - 2, 3): - nuc_frame = substr[idx:idx + 3] - if nuc_frame.lower() in ["tag", "taa", "tga"]: - return True - return False - -## Returns true if there is a stop codon found spanning the two sequences -# seq_prop: Propagating sequence -# seq_accept: Accepting sequence -# read_frame: Read frame of propagating vertex -# strand: Direction of read strand -def has_stop_codon_cross(seq_prop, seq_accept, read_frame, strand): - if strand == "+": - check_seq = seq_prop[-read_frame:] + seq_accept - else: # strand=="-" - check_seq = seq_prop[::-1][-read_frame:] + seq_accept[::-1] - for idx in range(0, len(check_seq) - 2, 3): - nuc_frame = check_seq[idx:idx + 3] - if nuc_frame.lower() in ["tag", "taa", "tga"]: - return True - return False + +def get_exon_dict(metadata_list): + """ Get an auxiliary dictionary used for filtering + + Parameters + ---------- + metadata_list: List(str). Returned by `calculate_output_peptide` + + Returns + ------- + exon_dict: dict. (read_frame, pos_mid_1, pos_mid_2, variant_combination) + -> List[Tuple(output_idx, pos_start, pos_end,)] + """ + exon_dict = {} + for line in metadata_list: + items = line.strip().split('\t') + ## TODO: need to come up with a new way to index the exon list + exon_list = items[-4].split(';') + idx = items[0] + read_frame = items[1] + strand = items[4] + if strand == '+': + key = (read_frame,exon_list[1],exon_list[2]) + if key in exon_dict: + exon_dict[key].append((idx, exon_list[0],exon_list[3])) + else: + exon_dict[key] = [(idx, exon_list[0],exon_list[3])] + else: + key = (read_frame,exon_list[3], exon_list[0]) + if key in exon_dict: + exon_dict[key].append((idx, exon_list[2], exon_list[1])) + else: + exon_dict[key] = [(idx, exon_list[2], exon_list[1])] + return exon_dict + + +def get_remove_id(metadata_dict): + # Todo: [Warning!] if two output lines have identical + # coordinates and readframe + # both of them will be removed. Need to fix. + remove_id_list = [] + for exon_pair_list in metadata_dict.values(): + L = len(exon_pair_list) + if L < 2: + continue + for i, exon_pair in enumerate(exon_pair_list): + for j in range(L): + i_pos1 = exon_pair[1] + i_pos2 = exon_pair[2] + j_pos1 = exon_pair_list[j][1] + j_pos2 = exon_pair_list[j][2] + if j!=i and i_pos1 >= j_pos1 and i_pos2 <= j_pos2: + remove_id_list.append(exon_pair[0]) + break + return remove_id_list + + +def get_filtered_output_list(metadata_list,peptide_list): + """ Get all redundant output id. + + Parameters + ---------- + metadata_dict: Dict. Returned by get_exon_dict + + Returns + ------- + remove_id_list: List[str]. The list of id to be removed. + """ + exon_list = get_exon_dict(metadata_list) + remove_id_list = get_remove_id(exon_list) + filtered_meta_list = [] + filtered_peptide_list = [] + for i,imeta_line in enumerate(metadata_list): + items = imeta_line.strip().split('\t') + idx = items[0] + if idx not in remove_id_list: + filtered_meta_list.append(imeta_line) + filtered_peptide_list.append(peptide_list[i]) + return filtered_meta_list, filtered_peptide_list + + + diff --git a/immunopepper/immuno_model.py b/immunopepper/immuno_model.py index 0723e201..2956a634 100644 --- a/immunopepper/immuno_model.py +++ b/immunopepper/immuno_model.py @@ -1,157 +1,159 @@ +"""Contains all the output computation based on gene splicegraph""" from __future__ import print_function -# External libraries + import numpy as np import scipy as sp -# immuno module + from immuno_filter import junction_is_annotated, peptide_match, find_background_peptides from immuno_mutation import apply_germline_mutation,get_exon_som_dict,get_som_expr_dict,get_mut_comb -from utils import cross_peptide_result,is_isolated_cds,isolated_peptide_result,is_output_redundant,is_in_junction_list +from utils import cross_peptide_result,is_isolated_cds,isolated_peptide_result,is_in_junction_list,get_segment_expr from immuno_preprocess import search_edge_metadata_segmentgraph +from constant import NOT_EXIST -# Optimized annotation code that does not loop over the annotation but uses the lookup structure -# that was built from the only initial pass -# over the GFF annotation file -# gene: Gene structure -# seg_lookup_table: Segment lookup table based on Gene ID -# strain_idx_table: Look-up strain index based on donor ID. -# segment_expr_info: Segment expression information -# gene_cds_begin_dict: Look-up to retrieve CDS beginnings associated with a gene [dict] -# ref_seq: Nucleotide sequence of chromosome associated with gene [str] -# mut_seq: Mutated sequence of donor -# fa_ptr: File handle to the output FASTA file -# mutation_mode: Mutation mode in {both, germline_only, somatic_only, None} -# size_factor: the adjusted weight from libsize -def annotate_gene_opt(gene=None, ref_seq=None, gene_idx=None, - seg_lookup_table=None, edge_lookup_table=None, size_factor=None, junction_list=None, - segment_expr_info=None, edge_expr_info=None, transcript_to_cds_table=None, - gene_to_transcript_table=None, - mutation_mode=None, mutation_sub_dic_vcf=None, mutation_sub_dic_maf=None, - peptide_ptr=None, meta_ptr=None, log_ptr=None, is_filter=True, debug=False): - #junction_list = np.concatenate((junction_list,[['50197167','50198309','+']]),axis=0) +def calculate_output_peptide(gene=None, ref_seq=None, idx=None, + segments=None, edges=None, table=None,debug=False, size_factor=None, junction_list=None, + mutation=None): + """Calculte the output peptide for every exon-pairs in the splicegraph + Parameters + ---------- + gene: Object, returned by SplAdder. + ref_seq: Str, reference sequnce of specific chromosome + idx: Namedtuple Idx, has attribute idx.gene and idx.sample + segments: Namedtuple Segments, store segment expression information from count.hdf5. + has attribute ['expr', 'lookup_table']. + edges: Namedtuple Edges, store edges expression information from count.hdf5. + has attribute ['expr','lookup_table'] + table: Namedtuple GeneTable, store the gene-transcript-cds mapping tables derived + from .gtf file. has attribute ['gene_to_cds_begin', 'ts_to_cds', 'gene_to_cds'] + debug: bool. More detailed information will be printed when debugging. + size_factor: Scalar. To adjust the expression counts based on the external file `libsize.tsv` + junction_list: List. Work as a filter to indicate some exon pair has certain + ordinary intron which can be ignored further. + mutation: Namedtuple Mutation, store the mutation information of specific chromosome and sample. + has the attribute ['mode', 'maf_dict', 'vcf_dict'] + Returns + ------- + output_peptide_list: List[str]. Contain all the possible output peptide in the given splicegraph. + output_metadata_list: List[str]. Contain the correpsonding medata data for each output peptide. + total_expr: Float. The sum of all the expression counts which will be used for generating libsize.tsv + """ sg = gene.splicegraph gene.from_sparse() + total_expr = 0 - is_output = False output_id = 0 - gene.output_vertex_dict = {} + output_peptide_list = [] + output_metadata_list = [] # apply germline mutation # when germline mutation is applied, background_seq != ref_seq # otherwise, background_seq = ref_seq - if mutation_sub_dic_vcf is not None: - ref_mut_seq = apply_germline_mutation(ref_sequence=ref_seq, pos_start=gene.start, pos_end=gene.stop, - mutation_sub_dic_vcf=mutation_sub_dic_vcf) - background_seq = ref_mut_seq['germline'] - else: - background_seq = ref_seq + pos_start = np.min(sg.vertices[0]) + pos_end = np.max(sg.vertices[1]) + ref_mut_seq = apply_germline_mutation(ref_sequence=ref_seq, pos_start=pos_start, pos_end=pos_end, + mutation_sub_dic_vcf=mutation.vcf_dict) # apply somatic mutation # som_exp_dict: (mutation_position) |-> (expression) # exon_som_dict: (exon_id) |-> (mutation_postion) som_exp_dict, exon_som_dict = None,None - if mutation_sub_dic_maf is not None: - exon_som_dict = get_exon_som_dict(gene, mutation_sub_dic_maf.keys()) - if segment_expr_info is not None: - som_exp_dict = get_som_expr_dict(gene,mutation_sub_dic_maf.keys(),segment_expr_info,seg_lookup_table) + if mutation.maf_dict is not None: + exon_som_dict = get_exon_som_dict(gene, mutation.maf_dict.keys()) + if segments is not None: + som_exp_dict = get_som_expr_dict(gene, mutation.maf_dict.keys(), segments, idx) # find background peptide # if no germline mutation is applies, germline key still exists, equals to reference. # return the list of the background peptide for each transcript - background_pep_list = find_background_peptides(gene, background_seq, gene_to_transcript_table, - transcript_to_cds_table) + background_pep_list = find_background_peptides(gene, ref_mut_seq['background'], table.gene_to_ts, table.ts_to_cds) # check whether the junction (specific combination of vertices) also is annotated # as a junction of a protein coding transcript - junction_flag = junction_is_annotated(gene, gene_to_transcript_table, transcript_to_cds_table) - - f_isolated = open('isolated_stop.txt','a') - - for idx in gene.vertex_order: - n_read_frames = len(sg.reading_frames[idx]) - # no cds start, skip the vertex - if n_read_frames == 0: - continue - if is_isolated_cds(gene, idx): # if it is an isolated cds, we add a flag idx -1, translate and output it - gene.vertex_succ_list[idx].append('.') - for prop_vertex in gene.vertex_succ_list[idx]: - #mut_seq_dict = get_mut_seq_dict(background_seq, mutation_sub_dic_maf, exon_som_dict, idx, prop_vertex) - mut_seq_comb = get_mut_comb(mutation_sub_dic_maf, exon_som_dict, idx, prop_vertex) + junction_flag = junction_is_annotated(gene, table.gene_to_ts, table.ts_to_cds) + reading_frame_dict = dict(sg.reading_frames) + for v_id in gene.vertex_order: + n_read_frames = len(reading_frame_dict[v_id]) + if n_read_frames == 0: # no cds start, skip the vertex + continue + if is_isolated_cds(gene, v_id): # if it is an isolated cds, we add a flag NOT_EXIST, translate and output it + gene.vertex_succ_list[v_id].append(NOT_EXIST) + for prop_vertex in gene.vertex_succ_list[v_id]: + mut_seq_comb = get_mut_comb(exon_som_dict, v_id, prop_vertex) for variant_comb in mut_seq_comb: # go through each variant combination # Skip de-generate exons that contain less than one codon - if gene.vertex_len_dict[idx] < 3: + if gene.vertex_len_dict[v_id] < 3: continue - for read_frame in sorted(sg.reading_frames[idx]): + for read_frame_tuple in sorted(reading_frame_dict[v_id]): if debug: - print(idx, prop_vertex, variant_comb, read_frame) + print(v_id, prop_vertex, variant_comb, read_frame_tuple) peptide_weight = 1.0 / n_read_frames - if prop_vertex != '.': - cross_peptide_mut, cross_peptide_ref, \ - start_v1, stop_v1, start_v2, stop_v2, \ - has_stop_codon, is_isolated, next_reading_frame = cross_peptide_result(read_frame, gene.strand, variant_comb, mutation_sub_dic_maf,background_seq, sg.vertices[:, prop_vertex]) - if not has_stop_codon: - sg.reading_frames[prop_vertex].add(next_reading_frame) - else: - cross_peptide_mut, cross_peptide_ref, \ - start_v1, stop_v1, start_v2, stop_v2, \ - has_stop_codon, is_isolated = isolated_peptide_result(read_frame, gene.strand, variant_comb, mutation_sub_dic_maf,background_seq) - if not has_stop_codon: - f_isolated.write(gene.name + '\t' + str(idx) + '\n') - - # If cross junction peptide has a stop-codon in it, we will not output it for simplicity, also the frame + if prop_vertex != NOT_EXIST: + peptide, coord, flag, next_reading_frame = cross_peptide_result(read_frame_tuple, gene.strand, variant_comb, mutation.maf_dict, ref_mut_seq, sg.vertices[:, prop_vertex]) + if not flag.has_stop: + reading_frame_dict[prop_vertex].add(next_reading_frame) + else: + peptide, coord, flag = isolated_peptide_result(read_frame_tuple, gene.strand, variant_comb, mutation.maf_dict,ref_mut_seq) + + # If cross junction peptide has a stop-codon in it, the frame # will not be propagated because the read is truncated before it reaches the end of the exon. - # also in mutated mode, only output the case where ref is different from mutated - if cross_peptide_mut != cross_peptide_ref or mutation_mode == 'ref': - if is_filter: - is_redundant = is_output_redundant(gene, start_v1, stop_v1, start_v2, stop_v2) - if not is_filter or not is_redundant: - match_ts_list = peptide_match(background_pep_list, cross_peptide_mut) - peptide_is_annotated = len(match_ts_list) - if not is_isolated: - junction_anno_flag = int(junction_flag[idx, prop_vertex]) - if not junction_list is None: - if gene.strand == '+': - junctionOI_flag = is_in_junction_list(sg.vertices[:, idx], sg.vertices[:, prop_vertex], gene.strand, junction_list) - else: - junctionOI_flag = is_in_junction_list(sg.vertices[:, prop_vertex], sg.vertices[:, idx], gene.strand, junction_list) + # also in mutation mode, only output the case where ref is different from mutated + if peptide.mut != peptide.ref or mutation.mode == 'ref': + match_ts_list = peptide_match(background_pep_list, peptide.mut) + peptide_is_annotated = len(match_ts_list) + if not flag.is_isolated: + junction_anno_flag = int(junction_flag[v_id, prop_vertex]) + if junction_list is not None: + if gene.strand == '+': + junctionOI_flag = is_in_junction_list(sg.vertices[:, v_id], sg.vertices[:, prop_vertex], gene.strand, junction_list) else: - junctionOI_flag = '.' + junctionOI_flag = is_in_junction_list(sg.vertices[:, prop_vertex], sg.vertices[:, v_id], gene.strand, junction_list) else: - junction_anno_flag = '.' - junctionOI_flag = '.' - # Write the variant gene into the FASTA FP together with the donor ID - str_variant_comb = [str(ipos) for ipos in variant_comb] - if variant_comb != '.' and som_exp_dict is not None: # which means there do exist some mutation - seg_exp_variant_comb = [str(som_exp_dict[ipos]) for ipos in variant_comb] - else: - seg_exp_variant_comb = '.' # if no mutation, the segment expression is . - meta_header_line = "\t".join( - [str(gene_idx) + '.' + str(output_id), str(read_frame[2]), gene.name, gene.chr, gene.strand, - mutation_mode, "{:.3f}".format(peptide_weight), str(peptide_is_annotated), str(junction_anno_flag), - str(int(has_stop_codon)), str(junctionOI_flag), str(int(is_isolated)), - ';'.join(str_variant_comb), ';'.join(seg_exp_variant_comb)]) - is_output = True - meta_header_line += ('\t' + str(start_v1) + ";" + str(stop_v1)) - meta_header_line += (';' + str(start_v2) + ";" + str(stop_v2) + '\t') - meta_header_line += (str(idx) + ',' + str(prop_vertex) + '\t') - - # deal with expression data - if edge_lookup_table is not None and not is_isolated: - sorted_pos = sp.sort(np.array([start_v1 - 1, stop_v1, start_v2 - 1,stop_v2])) - edge_expr = search_edge_metadata_segmentgraph(gene, sorted_pos, edge_lookup_table, edge_expr_info) - # edge_expr = edge_expr*size_factor - else: - edge_expr = '.' - meta_header_line += ("\t" .join(str(edge_expr))) - meta_ptr.write(meta_header_line + "\n") - peptide_str_pretty = '>' + str(gene_idx) + '.' + str(output_id) + '\n' + cross_peptide_mut - peptide_ptr.write(peptide_str_pretty + "\n") - output_id += 1 + junctionOI_flag = NOT_EXIST + else: + junction_anno_flag = NOT_EXIST + junctionOI_flag = NOT_EXIST + # Write the variant gene into the FASTA FP together with the donor ID + str_variant_comb = [str(ipos) for ipos in variant_comb] + + if variant_comb != NOT_EXIST and som_exp_dict is not None: # which means there do exist some mutation + seg_exp_variant_comb = [str(int(som_exp_dict[ipos])) for ipos in variant_comb] + else: + seg_exp_variant_comb = NOT_EXIST # if no mutation or no count file, the segment expression is . + + if segments is not None: + segment_expr = get_segment_expr(gene, coord, segments, idx) + else: + segment_expr = NOT_EXIST + + meta_header_line = "\t".join( + [str(idx.gene) + '.' + str(output_id), str(read_frame_tuple[2]), gene.name, gene.chr, gene.strand, + mutation.mode, "{:.3f}".format(peptide_weight), str(peptide_is_annotated), str(junction_anno_flag), + str(int(flag.has_stop)), str(junctionOI_flag), str(int(flag.is_isolated)), + ';'.join(str_variant_comb), ';'.join(seg_exp_variant_comb)]) + + meta_header_line += ('\t' + str(coord.start_v1) + ";" + str(coord.stop_v1)) + meta_header_line += (';' + str(coord.start_v2) + ";" + str(coord.stop_v2) + '\t') + meta_header_line += (str(v_id) + ',' + str(prop_vertex) + '\t') + + # deal with expression data + if edges is not None and not flag.is_isolated: + sorted_pos = sp.sort(np.array([coord.start_v1, coord.stop_v1, coord.start_v2, coord.stop_v2])) + edge_expr = search_edge_metadata_segmentgraph(gene, sorted_pos, edges, idx) + total_expr += edge_expr + #edge_expr = edge_expr*size_factor + else: + edge_expr = NOT_EXIST + meta_header_line += ("\t" .join([str(edge_expr)])) + meta_header_line += "\t"+str(segment_expr) + + output_metadata_list.append(meta_header_line) + peptide_str_pretty = '>' + str(idx.gene) + '.' + str(output_id) + '\t' + gene.name + '\n' + peptide.mut + output_peptide_list.append(peptide_str_pretty) + output_id += 1 if not sg.edges is None: gene.to_sparse() gene.processed = True - if not is_output: - log_ptr.write(str(gene_idx) + '\t' + gene.name + '\n') - f_isolated.close() + return output_peptide_list,output_metadata_list,total_expr diff --git a/immunopepper/immuno_mutation.py b/immunopepper/immuno_mutation.py index a804bd7e..22405c50 100644 --- a/immunopepper/immuno_mutation.py +++ b/immunopepper/immuno_mutation.py @@ -1,116 +1,179 @@ -import numpy as np +"""Contain functions to deal with mutation""" import bisect +import sys +from collections import namedtuple + +from constant import NOT_EXIST +from immuno_preprocess import parse_mutation_from_maf,parse_mutation_from_vcf from utils import get_all_comb -# if is_code_somatic = False, the maf information would not be encoded, -# even the mutation mode includes 'somatic' -def apply_germline_mutation(ref_sequence, pos_start,pos_end,mutation_sub_dic_vcf): - ## Todo: actually we can apply slicing on the reference geen so that save the memory consumed - ## Todo: split into two functions: germline and somatic +import numpy as np + +Mutation = namedtuple('Mutation', ['vcf_dict', 'maf_dict', 'mode']) + + +def apply_germline_mutation(ref_sequence, pos_start, pos_end, mutation_sub_dic_vcf): + """Apply germline mutation on the reference sequence + + Parameters + ---------- + ref_sequence: str. reference sequence of certain chromosome. + pos_start: int. start position of sequence for applying germiline mutation. + pos_end: int. Ending position of sequence for applying germline mutation. + mutation_sub_dic_vcf: dict. (position) -> variant details + + Returns + ------- + output_seq: dict. (sequence_type) -> list[char]. output['ref'] is the original + reference sequence output['background'] is the germline-mutation-applied sequence + if .maf file (somatic mutation) exists while is original sequence if no somatic + information is available. + """ output_seq = {} output_seq['ref'] = ref_sequence # copy the reference - mut_seq = list(ref_sequence) # if no mutation infomation is provided - - variant_pos = [pos for pos in mutation_sub_dic_vcf.keys()] - variant_pos_candi = [ipos for ipos in variant_pos if ipos > pos_start and ipos < pos_end] - - for variant_ipos in variant_pos_candi: - ref_base = mutation_sub_dic_vcf[variant_ipos]['ref_base'] - mut_base = mutation_sub_dic_vcf[variant_ipos]['mut_base'] - # print ref_sequence[variant_ipos] - # print ref_base - #assert ref_sequence[variant_ipos] == ref_base - mut_seq[variant_ipos] = mut_base - output_seq['germline'] = ''.join(mut_seq) + if mutation_sub_dic_vcf is not None: + mut_seq = construct_mut_seq_with_str_concat(ref_sequence, pos_start, pos_end, mutation_sub_dic_vcf) + output_seq['background'] = mut_seq + else: + output_seq['background'] = ref_sequence return output_seq -def apply_somatic_mutation(ref_sequence,all_comb, mutation_sub_dic_maf): - output_seq = {} - output_seq['.'] = ref_sequence - for icomb in all_comb: - mut_seq = list(ref_sequence) - # print(pos_start, pos_end, icomb) - for variant_ipos in icomb: - ref_base = mutation_sub_dic_maf[variant_ipos]['ref_base'] - mut_base = mutation_sub_dic_maf[variant_ipos]['mut_base'] - strand = mutation_sub_dic_maf[variant_ipos]['strand'] - variant_Classification = mutation_sub_dic_maf[variant_ipos]['variant_Classification'] - variant_Type = mutation_sub_dic_maf[variant_ipos]['variant_Type'] - # assert ref_sequence[variant_ipos] == ref_base - mut_seq[variant_ipos] = mut_base - output_seq[icomb] = ''.join(mut_seq) - return output_seq -def get_mutation_mode_from_parser(args): - flag = 0 - if len(args.vcf_path) == 0: - vcf_path = '' +def construct_mut_seq_with_str_concat(ref_seq, pos_start, pos_end, mut_dict): + """ Applying germline mutation on given range and get mutated sequence + + Parameters + ---------- + ref_seq: str. reference sequence + pos_start: int. Start position of applying germline mutation + pos_end: int. Stop position of applying germline mutation + mut_dict: dict. Germline mutation dictioanry + + Returns + ------- + mut_seq: str. mutation sequence + """ + variant_pos_candi = [ipos for ipos in mut_dict.keys() if ipos > pos_start and ipos < pos_end] + if len(variant_pos_candi) > 0: + variant_pos_sorted = np.sort(variant_pos_candi) + mut_seq_list = [ref_seq[:variant_pos_sorted[0]]] + for i in range(len(variant_pos_sorted)-1): # process all the mutation in order except the last one + mut_base = mut_dict[variant_pos_sorted[i]]['mut_base'] + ref_base = mut_dict[variant_pos_sorted[i]]['ref_base'] + if mut_base != '*': + mut_seq_list.append(mut_base) + else: + mut_seq_list.append(ref_base) + mut_seq_list.append(ref_seq[variant_pos_sorted[i]+1:variant_pos_sorted[i+1]]) + # process the last mutation separately + mut_base = mut_dict[variant_pos_sorted[-1]]['mut_base'] + ref_base = mut_dict[variant_pos_sorted[-1]]['ref_base'] + if mut_base != '*': + mut_seq_list.append(mut_base) + else: + mut_seq_list.append(ref_base) + mut_seq_list.append(ref_seq[variant_pos_sorted[-1]+1:]) + mut_seq = ''.join(mut_seq_list) else: - vcf_path = args.vcf_path[0] - flag += 1 + mut_seq = ref_seq + return mut_seq + - if len(args.maf_path) == 0: - maf_path = '' +def get_mutation_mode_from_parser(args): + Mutation = namedtuple('Mutation', ['mode','maf_dict','vcf_dict']) + mutation_mode = args.mutation_mode + maf_file_path = args.maf_path + vcf_file_path = args.vcf_path + is_error = True + if mutation_mode == 'somatic_and_germline': + if maf_file_path != '' and vcf_file_path != '': + mutation_dic_maf = parse_mutation_from_maf(maf_file_path) + mutation_dic_vcf = parse_mutation_from_vcf(vcf_file_path,args.samples, args.heter_code) + is_error = False + elif mutation_mode == 'germline': + if vcf_file_path != '': + mutation_dic_maf = {} # empty dic + mutation_dic_vcf = parse_mutation_from_vcf(vcf_file_path,args.samples, args.heter_code) + is_error = False + elif mutation_mode == 'somatic': + if maf_file_path != '': + mutation_dic_maf = parse_mutation_from_maf(maf_file_path) + mutation_dic_vcf = {} + is_error = False + elif mutation_mode == 'ref': + mutation_dic_maf = {} + mutation_dic_vcf = {} + is_error = False else: - maf_path = args.maf_path - flag += 2 - map_dict = {0:'ref', 1:'germline', 2:'somatic', 3:'somatic_and_germline'} - mutation_mode = map_dict[flag] - return mutation_mode, vcf_path, maf_path + print('Mutation mode "%s" not recognized' % mutation_mode) -def get_exon_som_dict(gene,mutation_pos): - seg_mat = gene.segmentgraph.segments[0] - seg_exon_mat = gene.segmentgraph.seg_match - exon_som_dict = {k:[] for k in range(seg_exon_mat.shape[0])} + if is_error: + print("The input mutation file does not match the mutation mode (somatic, germline, somatic_and_germline), please check again") + sys.exit(1) + mutation = Mutation(mutation_mode,mutation_dic_maf,mutation_dic_vcf) + return mutation + + +def get_exon_som_dict(gene, mutation_pos): + """ + Build exon id (key) to somatic mutation position dictionary. + """ + exon_list = gene.splicegraph.vertices + exon_som_dict = {k:[] for k in range(exon_list.shape[1])} for ipos in mutation_pos: - seg_id = bisect.bisect(seg_mat,ipos) - if seg_id > 0 and ipos <= gene.segmentgraph.segments[1][seg_id-1]: # the mutation is within the pos - exon_list = np.where(seg_exon_mat[:,seg_id-1] == 1)[0] - for id_exon in exon_list: - exon_som_dict[id_exon].append(ipos) - exon_som_dict['.'] = [] # for single cds case + for i in range(exon_list.shape[1]): + if ipos in range(exon_list[0,i], exon_list[1,i]): + exon_som_dict[i].append(ipos) + exon_som_dict[NOT_EXIST] = [] # for single cds case return exon_som_dict -def get_som_expr_dict(gene,mutation_pos,expr_mat,gene_ids_seg): + +def get_som_expr_dict(gene, mutation_pos, segments, Idx): + """ + Build somatic mutation position(key) to expression data(value) dictionary. + """ seg_mat = gene.segmentgraph.segments[0] som_expr_dict = {} - seg_pos_list = gene_ids_seg[gene.name] + + seg_pos_list = segments.lookup_table[gene.name] for ipos in mutation_pos: seg_id = bisect.bisect(seg_mat,ipos) - if seg_id > 0 and ipos <= gene.segmentgraph.segments[1][seg_id-1]: # the mutation is within the pos - expr = expr_mat[seg_pos_list[seg_id-1]] + if seg_id > 0 and ipos <= gene.segmentgraph.segments[1][seg_id-1]: # the mutation is within the pos + expr = segments.expr[seg_pos_list[seg_id-1],Idx.sample] som_expr_dict[ipos] = expr return som_expr_dict -def get_mut_seq_dict(background_seq, mutation_sub_dic_maf, exon_som_dict, idx, prop_vertex): - """ - Get sequence list when applied all the mutation combinations +def get_mut_comb(exon_som_dict, idx, prop_vertex): + """ + Get all the mutation combination given the mutation given. Parameters ---------- - background_seq: str, background_seq - mutation_sub_dic_maf: somatic mutation dict, {mutation_position:mutation_detail} - exon_som_dict: dict, {exon_id:mutation_position} - idx: int, vertex index - prop_vertex: int, next vertex index + exon_som_dict: dict, keys (exon id), values (somatic mutation position) + idx: int, first exon id + prop_vertex: int, second exon id Returns ------- + mut_comb: list of tuple, list of mutation combination """ - mut_seq_dict = {'.': background_seq} - if mutation_sub_dic_maf is not None: - all_comb = get_all_comb(exon_som_dict[idx] + exon_som_dict[prop_vertex]) - if len(all_comb) > 0: - mut_seq_dict = apply_somatic_mutation(ref_sequence=background_seq, all_comb=all_comb, - mutation_sub_dic_maf=mutation_sub_dic_maf) - return mut_seq_dict - - -def get_mut_comb(mutation_sub_dic_maf, exon_som_dict, idx, prop_vertex): - mut_comb = ['.'] - if mutation_sub_dic_maf is not None: + mut_comb = [NOT_EXIST] + if exon_som_dict is not None: all_comb = get_all_comb(exon_som_dict[idx] + exon_som_dict[prop_vertex]) mut_comb += all_comb return mut_comb + +def get_sub_mutation_tuple(mutation, sample, chrm): + """ Get sub mutation namedtuple on given sample and chromosome """ + if (sample, chrm) in mutation.vcf_dict.keys(): + mutation_sub_dict_vcf = mutation.vcf_dict[(sample, chrm)] + else: + mutation_sub_dict_vcf = None + if (sample, chrm) in mutation.maf_dict.keys(): + mutation_sub_dict_maf = mutation.maf_dict[(sample, chrm)] + else: + mutation_sub_dict_maf = None + submutation = Mutation(mutation_sub_dict_vcf,mutation_sub_dict_maf,mutation.mode) + return submutation diff --git a/immunopepper/immuno_preprocess.py b/immunopepper/immuno_preprocess.py index 0561c106..824201e3 100644 --- a/immunopepper/immuno_preprocess.py +++ b/immunopepper/immuno_preprocess.py @@ -1,26 +1,28 @@ -# python library -import timeit -import cPickle -import os -import csv +"""Contain the functions to parse, preprocess information from the input file""" import sys +from collections import namedtuple -# external library import numpy as np import h5py import scipy as sp -# immuno module -from immuno_print import print_memory_diags -from utils import to_adj_succ_list,find_overlapping_cds_simple,attribute_list_to_dict,leq_strand,encode_chromosome +from utils import to_adj_succ_list,find_overlapping_cds_simple,leq_strand,encode_chromosome + +GeneTable = namedtuple('GeneTable', ['gene_to_cds_begin', 'ts_to_cds', 'gene_to_ts']) +Segments = namedtuple('Segments', ['expr', 'lookup_table']) +Edges = namedtuple('Edges', ['expr', 'lookup_table']) +CountInfo = namedtuple('CountInfo', ['segments', 'edges', 'strain_idx_table']) -# Pre-process gene structures to aid fast generation of cross-junction peptides -# get gene.vertex_succ_list -# sort the vertex -# get gene.splicegraph.reading_frames -def genes_preprocess(genes, gene_cds_begin_dict): - f_log = open('cds_match_log.txt','w') +def genes_preprocess(genes, gene_cds_begin_dict): + """ Preprocess the gene and generate new attributes under gene object + Modify the gene object directly + + Parameters + ---------- + genes: List[Object]. List of gene objects. The object is generated by SplAdder + gene_cds_begin_dict: Dict. str -> List(int) From gene name to list of cds start positions + """ for gene_idx in range(genes.shape[0]): if gene_idx > 0 and gene_idx % 100 == 0: sys.stdout.write('.') @@ -63,23 +65,14 @@ def genes_preprocess(genes, gene_cds_begin_dict): cds_left = int(line_elems[3])-1 cds_right = int(line_elems[4]) - #TODO: need to remove the redundance of (cds_start,cds_stop,item) + #TODO: need to remove the redundance of (cds_start, cds_stop, item) # It's ugly and not necessary if gene.strand == "-": cds_right_modi = cds_right - cds_phase - #assert (cds_left == v_start) - #if cds_left != v_start: - # f_log.write(';'.join([str(gene_idx),str(idx)])+'\n') - #cds_left_modi = cds_left - ### we start at the annotated CDS start, but ignore annotated stops and take the sequence instead cds_left_modi = v_start n_trailing_bases = cds_right_modi - cds_left_modi - else: # gene.strand=="+": + else: cds_left_modi = cds_left + cds_phase - #assert (cds_right == v_stop) - #if cds_right != v_stop: - # f_log.write(';'.join([str(gene_idx),str(idx)])+'\n') - #cds_right_modi = cds_right cds_right_modi = v_stop n_trailing_bases = cds_right_modi - cds_left_modi @@ -89,52 +82,59 @@ def genes_preprocess(genes, gene_cds_begin_dict): gene.splicegraph.reading_frames[idx].add((cds_left_modi, cds_right_modi, read_phase)) gene.to_sparse() - f_log.close() -# Pre-processed the annotation file and builds a lookup structure that can be used to retrieve -# the CDS start positions when looping over the genes -##TODO: do we really need so many dictionary? + def preprocess_ann(ann_path): + """ Extract information from annotation file (.gtf, .gff and .gff3) + + Parameters + ---------- + ann_path: str. Annotation file path + Returns + ------- + gene_table: NamedTuple.store the gene-transcript-cds mapping tables derived + from .gtf file. has attribute ['gene_to_cds_begin', 'ts_to_cds', 'gene_to_cds'] + """ transcript_to_gene_dict = {} # transcript -> gene id gene_to_transcript_dict = {} # gene_id -> list of transcripts transcript_to_cds_dict = {} # transcript -> list of CDS exons - transcript_cds_begin_dict = {} # transcript -> first exon of the CDS + transcript_cds_begin_dict = {} # transcript -> first exon of the CDS gene_cds_begin_dict = {} # gene -> list of first CDS exons + file_type = ann_path.split('.')[-1] + # collect information from annotation file - for line in open(ann_path, 'r'): - item = line.split('\t') + for line in open(ann_path): + if line[0] == '#': + continue + item = line.strip().split('\t') feature_type = item[2] - attribute_list = item[-1].split('; ') - attribute_dict = attribute_list_to_dict(attribute_list) - + attribute_item = item[-1] + attribute_dict = attribute_item_to_dict(attribute_item, file_type, feature_type) # store relationship between gene ID and its transcript IDs if feature_type in ['transcript', 'mRNA']: gene_id = attribute_dict['gene_id'] - # gene_type = attribute_dict['gene_type'] - # transcript_type = attribute_dict['transcript_type'] - transcript_id = attribute_dict['transcript_id'] + if attribute_dict['gene_type'] != 'protein_coding' or attribute_dict['transcript_type'] != 'protein_coding': + continue assert (transcript_id not in transcript_to_gene_dict) transcript_to_gene_dict[transcript_id] = gene_id - - try: + if gene_id in gene_to_transcript_dict: gene_to_transcript_dict[gene_id].add(transcript_id) - except KeyError: - gene_to_transcript_dict[gene_id] = set([transcript_id]) + else: + gene_to_transcript_dict[gene_id] = {transcript_id} # Todo python is 0-based while gene annotation file(.gtf, .vcf, .maf) is one based - # so we need to do a little modification elif feature_type == "CDS": parent_ts = attribute_dict['transcript_id'] strand_mode = item[6] cds_left = int(item[3])-1 cds_right = int(item[4])-1 frameshift = int(item[7]) - try: + if parent_ts in transcript_to_cds_dict: transcript_to_cds_dict[parent_ts].append((cds_left, cds_right, frameshift)) - except KeyError: + else: transcript_to_cds_dict[parent_ts] = [(cds_left, cds_right, frameshift)] if strand_mode == "+" : cds_start, cds_stop = cds_left, cds_right @@ -158,14 +158,72 @@ def preprocess_ann(ann_path): for ts_key in transcript_to_cds_dict: transcript_to_cds_dict[ts_key] = sorted(transcript_to_cds_dict[ts_key], key=lambda coordpair: coordpair[0]) - return gene_cds_begin_dict, gene_to_transcript_dict, transcript_to_cds_dict - - -def search_edge_metadata_segmentgraph(gene, sorted_pos, edge_lookup_table, edge_expr_info): - ''' Gives the ordered edge coordinates of the edge, return expression information of the edge''' + genetable = GeneTable(gene_cds_begin_dict, transcript_to_cds_dict, gene_to_transcript_dict) + return genetable + + +def attribute_item_to_dict(a_item, file_type, feature_type): + """ From attribute item in annotation file to get corresponding dictionary + + Parameters + ---------- + a_item: str. attribute item + file_type: str. Choose from {'gtf', 'gff', 'gff3'} + feature_type: str. Extract other fields. We only + consider 'CDS', 'mRNA' and 'transcript' + + Returns + ------- + gtf_dict: dict. store all the necessary data + + """ + gtf_dict = {} + if file_type == 'gtf': + attribute_list = a_item.split('; ') + for attribute_pair in attribute_list: + pair = attribute_pair.split(' ') + gtf_dict[pair[0]] = pair[1][1:-1] + elif file_type == 'gff3': + attribute_list = a_item.split(';') + for attribute_pair in attribute_list: + pair = attribute_pair.split('=') + gtf_dict[pair[0]] = pair[1] + elif file_type == 'gff': + gff_dict = {} + attribute_list = a_item.split(';') + for attribute_pair in attribute_list: + pair = attribute_pair.split('=') + gff_dict[pair[0]] = pair[1] # delete "", currently now work on level 2 + if feature_type == 'CDS': + gtf_dict['transcript_id'] = gff_dict['Parent'] + elif feature_type in {'mRNA', 'transcript'}: # mRNA or transcript + gtf_dict['gene_id'] = gff_dict['geneID'] + gtf_dict['transcript_id'] = gff_dict['ID'] + gtf_dict['gene_type'] = gff_dict['gene_type'] + gtf_dict['transcript_type'] = gff_dict['transcript_type'] + + return gtf_dict + + +def search_edge_metadata_segmentgraph(gene, sorted_pos, edges, Idx): + """Given the ordered edge coordinates of the edge, return expression information of the edge + + Parameters + ---------- + gene: Object. Generated by SplAdder + sorted_pos: np.array of length 4. Sorted coordinates of 4 positions in ascending order + edges: namedtuple, store edges expression information from count.hdf5. + has attribute ['expr','lookup_table'] + idx: Namedtuple, has attribute idx.gene and idx.sample + + Returns + ------- + expr: float. Expression level for the given edges. + """ gene_name = gene.name segmentgraph = gene.segmentgraph - edge_idxs = edge_lookup_table[gene_name] + edge_idxs = edges.lookup_table[gene_name] + a = sp.where(segmentgraph.segments[1, :] == sorted_pos[1])[0] b = sp.where(segmentgraph.segments[0, :] == sorted_pos[2])[0] if a < b: @@ -175,38 +233,26 @@ def search_edge_metadata_segmentgraph(gene, sorted_pos, edge_lookup_table, edge_ cidxs = list(filter(lambda elem: elem[1] == idx, edge_idxs)) assert (len(cidxs) == 1) cidx = cidxs[0] - count = edge_expr_info[cidx[0]] + count = edges.expr[cidx[0], Idx.sample] return count -## Given a segment graph and a 1-based genomic coordinate position of a somatic mutation, returns the expression -# level of the one segment that contains the position. Performs a linear search in the segments contained in -# the graph. Could be optimized to do a binary search, let's see if it is a bottleneck. -def search_metadata_segmentgraph(gene, gen_coord, seg_lookup_table, strain_idx_table, segment_expr_info, donor_id, - sample_suffix=None): - gene_name = gene.name - segment_graph = gene.segmentgraph - seg_idxs = seg_lookup_table[gene_name] - col_idx = strain_idx_table[donor_id + sample_suffix] - assert (len(seg_idxs) == segment_graph.segments.shape[1]) - - # We use that in a segment graph, the vertices are not overlapping, so once we have found the segment, - # we can look-up its expression value and return directly. - for per_gene_idx, global_seg_idx in enumerate(seg_idxs): - lbound = segment_graph.segments[0, per_gene_idx] + 1 - rbound = segment_graph.segments[1, per_gene_idx] - - if gen_coord >= lbound and gen_coord <= rbound: - gene_expr_entry = float(segment_expr_info[global_seg_idx, col_idx]) - return gene_expr_entry, per_gene_idx - - assert (False) - return np.nan - -## Constructs look-up tables to lookup the correct column in matrix for a particular donor and -# splits the global segments matrix into smaller chunks for each geneID to enable faster look-up -# during peptide emission. -def parse_gene_metadata_info(h5f, donor_list): +def parse_gene_metadata_info(h5f, sample_list): + """ Parse the count file + + Parameters + ---------- + h5f: str. .count.h5f file + sample_list: List(str). List of samples. + + Returns + ------- + countinfo: Namedtuple. Store all the counts information. Has attributes + ['segments', 'edges', 'strain_id_table'], storing the segment expression + information, edge expression information and strain-id mapping. + strain-id mapping can tell us which column of segments or edges mat represent + which sample. + """ strain_expr_info = h5f["/strains"] segment_expr_info = h5f["/segments"] edge_expr_info = h5f["/edges"] @@ -214,11 +260,11 @@ def parse_gene_metadata_info(h5f, donor_list): assert (strain_expr_info.size == segment_expr_info.shape[1]) strain_idx_table = {} - for strain_idx in np.arange(strain_expr_info.size): - strain_id = strain_expr_info[strain_idx] - strain_id = '-'.join(strain_id.split('.')[0].split('-')[:3]) - if strain_id in donor_list: - strain_idx_table[strain_id] = strain_idx + for sample in sample_list: + for i, strain in enumerate(strain_expr_info): + if strain.startswith(sample): + strain_idx_table[sample] = i + continue gene_names = h5f["/gene_names"] gene_ids_segs = h5f["/gene_ids_segs"] @@ -228,6 +274,7 @@ def parse_gene_metadata_info(h5f, donor_list): seg_lookup_table = {} edge_lookup_table = {} + #print(gene_ids_segs.shape) for seg_idx in np.arange(gene_ids_segs.shape[0]): gene_id = gene_names[gene_ids_segs[seg_idx, 0]] if gene_id not in seg_lookup_table: @@ -240,9 +287,28 @@ def parse_gene_metadata_info(h5f, donor_list): edge_lookup_table[gene_id] = [] edge_lookup_table[gene_id].append((edge_idx, edge_idx_info[edge_idx])) - return (seg_lookup_table, edge_lookup_table, strain_idx_table, segment_expr_info, edge_expr_info) + segments = Segments(segment_expr_info,seg_lookup_table) + edges = Edges(edge_expr_info,edge_lookup_table) + countinfo = CountInfo(segments,edges,strain_idx_table) + return countinfo + -def parse_mutation_from_vcf(vcf_path): +def parse_mutation_from_vcf(vcf_path, sample_list=None, heter_code=0): + """Extract germline mutation information from the given vcf file and vcf.h5 file + + Parameters + ---------- + vcf_path: str, vcf file path + sample_list: list, list of samples + + Returns + ------- + mut_dict: with key (sample, chromo) and values (var_dict) + """ + file_type = vcf_path.split('.')[-1] + if file_type == 'h5': + mutation_dic = parse_mutation_from_vcf_h5(vcf_path,sample_list,heter_code) + return mutation_dic f = open(vcf_path,'r') lines = f.readlines() mutation_dic = {} @@ -261,43 +327,63 @@ def parse_mutation_from_vcf(vcf_path): var_dict['mut_base'] = items[4] var_dict['qual'] = items[5] var_dict['filter'] = items[6] - info = items[7] - info_items =info.split(';') - for info_item in info_items: - key, value = info_item.split('=') - if key == 'VT': - var_dict['varianttype'] = value - break - if var_dict['varianttype'] == 'SNP': # only consider snp for now - for sample_id in sample_list: # modify it when figuring out donor-variant in vcf - if (sample_id,chr) in mutation_dic.keys(): # use tuple of sample_id&chr as the key - mutation_dic[(sample_id,chr)][int(pos)] = var_dict - else: - mutation_dic[(sample_id,chr)] = {} - mutation_dic[(sample_id, chr)][int(pos)] = var_dict + if len(var_dict['ref_base']) == len(var_dict['mut_base']): # only consider snp for now + for i, sample_id in enumerate(sample_list): + if items[9+i].split(':')[0] in {'1|1' ,'1|0', '0|1'}: + if (sample_id,chr) in mutation_dic.keys(): + mutation_dic[(sample_id,chr)][int(pos)] = var_dict + else: + mutation_dic[(sample_id,chr)] = {} + mutation_dic[(sample_id, chr)][int(pos)] = var_dict return mutation_dic -def parse_mutation_from_vcf_h5(h5_vcf_path,donor_list): + +def parse_mutation_from_vcf_h5(h5_vcf_path, sample_list, heter_code=0): + """ + Extract germline mutation information from given vcf h5py file. + + Parameters + ---------- + h5_vcf_path: str, vcf file path + sample_list: list of str, list for sample name + + Returns + ------- + mut_dict: with key (sample, chromo) and values (var_dict) + + """ a = h5py.File(h5_vcf_path,'r') mut_dict = {} - for donor in donor_list: - col_id = [i for (i, item) in enumerate(a['gtid']) if item.startswith(donor)][0] - row_id = sp.where(a['gt'][:,col_id]==0)[0] + for sample in sample_list: + col_id = [i for (i, item) in enumerate(a['gtid']) if item.startswith(sample)][0] + row_id = sp.where(sp.logical_or(a['gt'][:,col_id] == heter_code,a['gt'][:,col_id] == 1))[0] for irow in row_id: - var_dict = {} chromo = encode_chromosome(a['pos'][irow,0]) pos = a['pos'][irow,1]-1 mut_base = a['allele_alt'][irow] ref_base = a['allele_ref'][irow] var_dict = {"mut_base":mut_base,"ref_base":ref_base} - if (donor,chromo) in mut_dict: - mut_dict[(donor,chromo)][pos] = var_dict + if (sample,chromo) in mut_dict: + mut_dict[(sample,chromo)][pos] = var_dict else: - mut_dict[(donor,chromo)] = {} - mut_dict[(donor,chromo)][pos] = var_dict + mut_dict[(sample,chromo)] = {} + mut_dict[(sample,chromo)][pos] = var_dict return mut_dict + def parse_mutation_from_maf(maf_path): + """ + Extract somatic mutation information from given maf file. + + Parameters + ---------- + maf_path: str, maf file path + + Returns + ------- + mut_dict: with key (sample, chromo) and values (var_dict) + + """ f = open(maf_path) lines = f.readlines() mutation_dic = {} @@ -305,7 +391,7 @@ def parse_mutation_from_maf(maf_path): print(i) items = line.strip().split('\t') if items[9] == 'SNP': # only consider snp - sample_id = '-'.join(items[15].split('-')[:3]) # or Tumor_Seq_Allele2 + sample_id = '-'.join(items[15].split('-')[:3]) chr = items[4] pos = int(items[5])-1 var_dict = {} @@ -321,8 +407,19 @@ def parse_mutation_from_maf(maf_path): mutation_dic[((sample_id,chr))][int(pos)] = var_dict return mutation_dic + def parse_junction_meta_info(h5f_path): - # jiayu Todo: can use binary search to improve + """ + Extract introns of interest from given h5py file + Parameters + ---------- + h5f_path: str, h5py file path + + Returns + ------- + junction_dict: dict, key (chromosome id), value (set of coordinate pairs) + + """ if h5f_path is None: return None else: @@ -337,20 +434,4 @@ def parse_junction_meta_info(h5f_path): junction_dict[ichr].add(':'.join([pos[i, 0], pos[i, 1], strand[i]])) except KeyError: junction_dict[ichr] = set([':'.join([pos[i, 0], pos[i, 1], strand[i]])]) - #if ichr not in junction_dict.keys(): - # junction_dict[ichr] = [(pos[i][0], pos[i][1], strand[i])] - #else: - # junction_dict[ichr].append((pos[i][0], pos[i][1], strand[i])) - #for key in junction_dict.keys(): - # junction_dict[key] = np.array(junction_dict[key]) return junction_dict - - - - - - - - - - diff --git a/immunopepper/immuno_print.py b/immunopepper/immuno_print.py index b9e3343b..1d56144b 100644 --- a/immunopepper/immuno_print.py +++ b/immunopepper/immuno_print.py @@ -1,15 +1,11 @@ import psutil import os -## Overview of somatic mutation information -def print_som_info(som_table): - for k, v in som_table.iteritems(): - print("Somatic mutations for donor: {}".format(k)) - - print("Number of mutations: {}".format(len(v))) def print_memory_diags(): - ''' Print memory diagnostics including the active resident set size''' + """ + Print memory diagnostics including the active resident set size + """ process = psutil.Process(os.getpid()) print('\tMemory usage: {:.3f} GB\n'.format(process.memory_info().rss/1000000000.0)) diff --git a/immunopepper/io_utils.py b/immunopepper/io_utils.py new file mode 100644 index 00000000..a593c3ed --- /dev/null +++ b/immunopepper/io_utils.py @@ -0,0 +1,27 @@ +import pickle + + +# TODO: this is a hack to get around module name changes spladder affecting pickle +def load_pickled_graph(f): + # following https://wiki.python.org/moin/UsingPickle/RenamingModules + renametable = { + 'modules.classes.gene': 'spladder.classes.gene', + 'modules.classes.splicegraph': 'spladder.classes.splicegraph', + 'modules.classes.segmentgraph': 'spladder.classes.segmentgraph' + } + + def mapname(name): + if name in renametable: + return renametable[name] + return name + + def mapped_load_global(self): + module = mapname(self.readline()[:-1]) + name = mapname(self.readline()[:-1]) + klass = self.find_class(module, name) + self.append(klass) + + unpickler = pickle.Unpickler(f) + + unpickler.dispatch[pickle.GLOBAL] = mapped_load_global + return unpickler.load() diff --git a/immunopepper/main_immuno.py b/immunopepper/main_immuno.py index 695819fa..10663f30 100644 --- a/immunopepper/main_immuno.py +++ b/immunopepper/main_immuno.py @@ -11,66 +11,50 @@ # External libraries import Bio.SeqIO as BioIO import h5py -import numpy as np + # immuno module -from immuno_print import print_memory_diags -from immuno_preprocess import genes_preprocess,preprocess_ann,parse_gene_metadata_info,parse_mutation_from_maf,parse_mutation_from_vcf_h5,parse_junction_meta_info -from immuno_mutation import get_mutation_mode_from_parser -from immuno_model import annotate_gene_opt -### Example usage -# python main_immuno.py --samples TCGA-13-1489 --output_dir t --splice_path quick_test_data/sample_gene.pkl --ann_path quick_test_data/small.gtf --ref_path quick_test_data/smallgene34.fa -# python exon_filter.py --meta_file t/TCGA-13-1489/ref_meta1.tsv.gz --peptide_file t/TCGA-13-1489/ref_peptide2.fa +from immunopepper.immuno_print import print_memory_diags +from immunopepper.immuno_preprocess import genes_preprocess,preprocess_ann,parse_gene_metadata_info,parse_junction_meta_info +from immunopepper.immuno_mutation import get_mutation_mode_from_parser,get_sub_mutation_tuple +from immunopepper.immuno_model import calculate_output_peptide +from immunopepper.immuno_filter import get_filtered_output_list +from immunopepper.io_utils import load_pickled_graph +from immunopepper.utils import get_idx,create_libsize + def parse_arguments(argv): - parser = argparse.ArgumentParser(argv) + parser = argparse.ArgumentParser() parser.add_argument("--samples", nargs='+', help="the sample names, can specify more than one sample", required=False, default='') - parser.add_argument("--output_dir", help="specify the output directory [default: test]", required=False, default='test') - parser.add_argument("--ann_path", help="specify the absolute path of annotation file", required=True) - parser.add_argument("--splice_path", help="specify the absolute path of splicegraph file", required=True) - parser.add_argument("--ref_path", help="specify the absolute path of reference gene file to the work_dir", required=True) + parser.add_argument("--output_dir", help="specify the output directory [default: tests]", required=False, default='test') + parser.add_argument("--ann_path", help="specify the absolute path of annotation file", required=False) + parser.add_argument("--splice_path", help="specify the absolute path of splicegraph file", required=False) + parser.add_argument("--ref_path", help="specify the absolute path of reference gene file to the work_dir", required=False) parser.add_argument("--libsize_path", nargs='?', help="specify the absolute path to expression library sizes",required=False, default=None) - parser.add_argument("--vcf_path", nargs=1, help="specify the absolute path of vcf file", required=False, default='') - parser.add_argument("--maf_path", nargs=1, help="specify the absolute path of maf file", required=False, default='') + parser.add_argument("--vcf_path", help="specify the absolute path of vcf file", required=False, default='') + parser.add_argument("--maf_path", help="specify the absolute path of maf file", required=False, default='') parser.add_argument("--count_path",help="specify the absolute path of the count h5 file", required=False, default=None) parser.add_argument("--gtex_junction_path",help="specify the absolute path the the gtex_junction h5 file", required=False, default=None) parser.add_argument("--process_num", type=int, help="Only process the first *process_num* gene in the splicegraph,default,0, means process all", required=False, default=0) - parser.add_argument("--is_filter", help="apply redundancy filter to the exon list", action="store_false", required=False, default=True) + parser.add_argument("--filter_redundant", help="apply redundancy filter to the exon list", action="store_true", required=False, default=False) parser.add_argument("--debug", help="generate debug output", action="store_true", required=False, default=False) - - + parser.add_argument("--mutation_mode", help="specify the mutation mdoe", required=False, default='ref') + parser.add_argument("--heter_code", type=int, help="if count expression data is provided in h5 format, specify the code for heterzygous", default=0) if len(argv) < 2: parser.print_help() sys.exit(1) - pargs = parser.parse_args() + pargs = parser.parse_args(argv) return pargs -def main(): - - arg = parse_arguments(sys.argv) - - ## for debugging in pycharm - # arg.output_dir = 'test' - # arg.ann_path = 'quick_test_data/small.gtf' - # arg.ref_path = 'quick_test_data/smallgene34.fa' - # arg.splice_path = 'quick_test_data/sample_gene.pkl' - # arg.gtex_junction_path = 'quick_test_data/gtex_junctions.hdf5' - # arg.vcf_path = 'quick_test_data/chrx.vcf' - # arg.maf_path = 'quick_test_data/chrx.maf' - # arg.samples = ['OMM475.T'] - - mutation_mode, vcf_file_path, maf_file_path = get_mutation_mode_from_parser(arg) - print(arg.samples) +def main(arg): # load genome sequence data seq_dict = {} start_time = timeit.default_timer() interesting_chr = map(str, range(1, 23)) + ["X", "Y", "MT"] - - # read reference genome for standard chromosomes print('Parsing genome sequence ...') for record in BioIO.parse(arg.ref_path, "fasta"): if record.id in interesting_chr: @@ -82,39 +66,24 @@ def main(): # read and process the annotation file print('Building lookup structure ...') start_time = timeit.default_timer() - gene_cds_begin_dict, gene_to_transcript_table, transcript_to_cds_table = preprocess_ann(arg.ann_path) + genetable = preprocess_ann(arg.ann_path) end_time = timeit.default_timer() print('\tTime spent: {:.3f} seconds'.format(end_time - start_time)) print_memory_diags() # read the variant file - if mutation_mode == 'somatic_and_germline': - mutation_dic_maf = parse_mutation_from_maf(maf_file_path) - mutation_dic_vcf = parse_mutation_from_vcf_h5(vcf_file_path, arg.samples) - elif mutation_mode == 'germline': - mutation_dic_maf = {} # empty dic - mutation_dic_vcf = parse_mutation_from_vcf_h5(vcf_file_path, arg.samples) - elif mutation_mode == 'somatic': - mutation_dic_maf = parse_mutation_from_maf(maf_file_path) - mutation_dic_vcf = {} # empty dic - elif mutation_mode == 'ref': - mutation_dic_maf = {} - mutation_dic_vcf = {} - else: - print('Mutation mode "%s" not recognized' % mutation_mode) - sys.exit(1) + mutation = get_mutation_mode_from_parser(arg) - # Personalized analysis # load splicegraph print('Loading splice graph ...') start_time = timeit.default_timer() with open(arg.splice_path, 'r') as graph_fp: - (graph_data, graph_meta) = cPickle.load(graph_fp) # both graph data and meta data + (graph_data, graph_meta) = load_pickled_graph(graph_fp) # both graph data and meta data end_time = timeit.default_timer() print('\tTime spent: {:.3f} seconds'.format(end_time - start_time)) print_memory_diags() - - if arg.process_num == 0: # Default process all genes + + if arg.process_num == 0: # Default process all genes num = len(graph_data) else: num = arg.process_num @@ -124,23 +93,22 @@ def main(): if arg.count_path is not None: print('Loading count data ...') h5f = h5py.File(arg.count_path, 'r') - seg_lookup_table, edge_lookup_table, strain_idx_table, segment_expr_info, edge_expr_info = parse_gene_metadata_info(h5f, arg.samples) + countinfo = parse_gene_metadata_info(h5f, arg.samples) + edges, segments, strain_idx_table = countinfo.edges,countinfo.segments,countinfo.strain_idx_table end_time = timeit.default_timer() print('\tTime spent: {:.3f} seconds'.format(end_time - start_time)) print_memory_diags() # get the fp #strains = sp.array([x.split('.')[0] for x in h5f['strains'][:]]) #size_factor = get_size_factor(strains, arg.libsize_path) - size_factor = None + #size_factor = None else: - seg_lookup_table = None - edge_lookup_table = None + segments = None + edges = None strain_idx_table = None - segment_expr_info = None - edge_expr_info = None size_factor = None - # read the intro of interest file gtex_junctions.hdf5 + # read the intron of interest file gtex_junctions.hdf5 junction_dict = parse_junction_meta_info(arg.gtex_junction_path) # process the genes according to the annotation file @@ -148,91 +116,75 @@ def main(): print('Processing gene set ...') start_time = timeit.default_timer() anno_pickle = os.path.join(arg.output_dir, 'annotation_preprop.pickle') - if os.path.exists(anno_pickle): + if os.path.exists(anno_pickle) and not arg.debug: print('...loading from preprocessed dump: %s' % anno_pickle) (graph_data, gene_cds_begin_dict) = cPickle.load(open(anno_pickle, 'r')) else: print('...computing from annotation') - genes_preprocess(graph_data, gene_cds_begin_dict) - if not os.path.exists(arg.output_dir): - os.makedirs(arg.output_dir) - cPickle.dump((graph_data, gene_cds_begin_dict), open(anno_pickle, 'w'), -1) + genes_preprocess(graph_data, genetable.gene_to_cds_begin) + cPickle.dump((graph_data, genetable.gene_to_cds_begin), open(anno_pickle, 'w'), -1) end_time = timeit.default_timer() print('\tTime spent: {:.3f} seconds'.format(end_time - start_time)) + expr_distr_dict = {} + expr_distr = [] # process graph for each input sample + output_libszie_fp = os.path.join(arg.output_dir,'expression_counts.libsize.tsv') for sample in arg.samples: # prepare for the output file output_path = os.path.join(arg.output_dir, sample) if not os.path.isdir(output_path): os.makedirs(output_path) - peptide_file_path = os.path.join(output_path, mutation_mode + '_peptides.fa') - meta_peptide_file_path = os.path.join(output_path, mutation_mode + '_metadata.tsv.gz') - log_file_path = os.path.join(output_path, mutation_mode+'_no_output_gene.txt') - log_fp = open(log_file_path, 'w') + peptide_file_path = os.path.join(output_path, mutation.mode + '_peptides.fa') + meta_peptide_file_path = os.path.join(output_path, mutation.mode + '_metadata.tsv.gz') peptide_fp = open(peptide_file_path, 'w') meta_peptide_fp = gzip.open(meta_peptide_file_path, 'w') meta_header_line = "\t".join(['output_id','read_frame','gene_name', 'gene_chr', 'gene_strand','mutation_mode','peptide_weight','peptide_annotated', - 'junction_annotated','has_stop_codon','is_in_junction_list','is_isolated','variant_comb','seg_expr', 'exons_coor', 'vertex_idx','junction_expr']) + 'junction_annotated','has_stop_codon','is_in_junction_list','is_isolated','variant_comb','variant_seg_expr', + 'exons_coor', 'vertex_idx','junction_expr','segment_expr']) meta_peptide_fp.write(meta_header_line + '\n') - + expr_distr_dict[sample] = [] # go over each gene in splicegraph for gene_idx, gene in enumerate(graph_data[:num]): start_time = timeit.default_timer() print('%s %i/%i\n'%(sample, gene_idx, num)) - gene = graph_data[gene_idx] + idx = get_idx(strain_idx_table,sample,gene_idx) # Genes not contained in the annotation... - if gene.name not in gene_cds_begin_dict or gene.name not in gene_to_transcript_table: + if gene.name not in genetable.gene_to_cds_begin or gene.name not in genetable.gene_to_ts: gene.processed = False continue chrm = gene.chr.strip() - if (sample, chrm) in mutation_dic_vcf.keys(): - mutation_sub_dict_vcf = mutation_dic_vcf[(sample, chrm)] - else: - mutation_sub_dict_vcf = None - if (sample, chrm) in mutation_dic_maf.keys(): - mutation_sub_dict_maf = mutation_dic_maf[(sample, chrm)] - else: - mutation_sub_dict_maf = None - - if segment_expr_info is not None: - sub_segment_expr_info = segment_expr_info[:, strain_idx_table[sample]] - sub_edge_expr_info = edge_expr_info[:, strain_idx_table[sample]] - else: - sub_segment_expr_info = None - sub_edge_expr_info = None - + sub_mutation = get_sub_mutation_tuple(mutation,sample, chrm) if not junction_dict is None and chrm in junction_dict: junction_list = junction_dict[chrm] else: junction_list = None - annotate_gene_opt(gene=gene, + output_peptide_list, output_metadata_list, total_expr = calculate_output_peptide(gene=gene, ref_seq=seq_dict[chrm], - gene_idx=gene_idx, - seg_lookup_table=seg_lookup_table, - edge_lookup_table=edge_lookup_table, - size_factor=size_factor, - junction_list=junction_list, - segment_expr_info=sub_segment_expr_info, - edge_expr_info=sub_edge_expr_info, - transcript_to_cds_table=transcript_to_cds_table, - gene_to_transcript_table=gene_to_transcript_table, - mutation_mode=mutation_mode, - mutation_sub_dic_vcf=mutation_sub_dict_vcf, - mutation_sub_dic_maf=mutation_sub_dict_maf, - peptide_ptr=peptide_fp, - meta_ptr=meta_peptide_fp, - log_ptr=log_fp, - is_filter=arg.is_filter, - debug=arg.debug + idx=idx, segments=segments, edges=edges, + table=genetable, mutation=sub_mutation, + junction_list=junction_list, debug=arg.debug ) - + expr_distr.append(total_expr) + if arg.filter_redundant: + output_metadata_list, output_peptide_list = get_filtered_output_list(output_metadata_list,output_peptide_list) + assert len(output_metadata_list) == len(output_peptide_list) + if len(output_peptide_list) > 0: + meta_peptide_fp.write('\n'.join(output_metadata_list)+'\n') + peptide_fp.write('\n'.join(output_peptide_list)+'\n') end_time = timeit.default_timer() print(gene_idx, end_time - start_time,'\n') + expr_distr_dict[sample] = expr_distr + create_libsize(expr_distr_dict,output_libszie_fp) + + +def cmd_entry(): + arg = parse_arguments(sys.argv[1:]) + main(arg) if __name__ == "__main__": - main() + cmd_entry() diff --git a/immunopepper/utils.py b/immunopepper/utils.py index 14888c5a..1f68e5f7 100644 --- a/immunopepper/utils.py +++ b/immunopepper/utils.py @@ -1,10 +1,23 @@ +"""Contain functions to help compute, to preprocess""" import itertools - import scipy as sp import numpy as np -# Converts a binary adjacency matrix to a list of directed edges +from collections import namedtuple +import bisect + +from constant import NOT_EXIST + +Peptide = namedtuple('Peptide', ['mut', 'ref']) +Coord = namedtuple('Coord', ['start_v1', 'stop_v1', 'start_v2', 'stop_v2']) +Flag = namedtuple('Flag', ['has_stop', 'is_isolated']) +Idx = namedtuple('Idx', ['gene', 'sample']) + + def to_adj_list(adj_matrix): + """ + Converts a binary adjacency matrix to a list of directed edges + """ adj_list = [] assert (adj_matrix.shape[0] == adj_matrix.shape[1]) for idx in range(adj_matrix.shape[0]): @@ -13,8 +26,22 @@ def to_adj_list(adj_matrix): adj_list.append([idx, jdx]) return adj_list -# Returns a list of successors by vertex, sensitive to the read strand + def to_adj_succ_list(adj_matrix, vertex_map, read_strand): + """ Returns a list of successors by vertex, sensitive to the read strand + + Parameters + ---------- + adj_matrix: 2D array with size [len(edges),len(edges)]. '1' represents the two edges + are connected. + vertex_map: 2D array with size [2, len(vertexs)]. Vertex positions + read_strand: The gene strand. '+' or '-'. + + Returns + ------- + succ_list: List[List[int]]. The connected vertex list for each vertex + + """ succ_list = [] assert (adj_matrix.shape[0] == adj_matrix.shape[1]) for idx in range(adj_matrix.shape[0]): @@ -27,59 +54,55 @@ def to_adj_succ_list(adj_matrix, vertex_map, read_strand): return succ_list -# Find overlapping CDS given a list of CDS starts def find_overlapping_cds_simple(v_start, v_stop, cds_begins, strand): - if strand == "+": - return filter(lambda cds_begin: cds_begin[0] >= v_start and cds_begin[1] <= v_stop, cds_begins) - else: - return filter(lambda cds_begin: cds_begin[1] >= v_start and cds_begin[0] <= v_stop, cds_begins) - - -def attribute_list_to_dict(a_list): - a_dict = {} - for attribute_pair in a_list: - pair = attribute_pair.split(' ') - a_dict[pair[0]] = pair[1][1:-1] # delete "", currently now work on level 2 - return a_dict + """ + Find overlapping CDS within an exon given a list of CDS starts + """ + # cds_start = cds_begin[0] + return filter(lambda cds_begin: cds_begin[0] >= v_start and cds_begin[0] <= v_stop, cds_begins) -# Returns strand-sensitive order between two genomic coordinates -def leq_strand(coord1, coord2, strand_mode): - if strand_mode == "+": +def leq_strand(coord1, coord2, strand): + if strand == "+": return coord1 <= coord2 - else: # strand_mode == "-" + else: return coord1 >= coord2 -# Yields the complementary DNA sequence -# dna_seq: Input nucleotide sequence + def complementary_seq(dna_seq): + """ Yields the complementary DNA sequence + Only convert the character in comp_dict. + Otherwise remain the same. + """ comp_dict = {"A": "T", "T": "A", "C": "G", "G": "C"} comp_dict_keys = comp_dict.keys() return "".join(map(lambda nuc: comp_dict[nuc] if nuc in comp_dict_keys else nuc, dna_seq)) -# Returns header labels corresponding to donor_id and mutation_mode -def header_labels(donor_id, mutation_mode): - if mutation_mode is None: - mutation_type = "REFERENCE" - elif mutation_mode == "both": - mutation_type = "GERM_SOMATIC" - elif mutation_mode == "somatic_only": - mutation_type = "SOMATIC" - elif mutation_mode == "germline_only": - mutation_type = "GERM" - - peptide_type = "REFERENCE" if donor_id == "ref" else donor_id - - return (peptide_type, mutation_type) - -# Encodes chromosome to same cn def encode_chromosome(in_num): + """ + Encodes chromosome to same cn + """ convert_dict = {23: "X", 24: "Y", 25: "MT"} return convert_dict[in_num] if in_num in convert_dict.keys() else str(in_num) -# Translate a DNA sequence encoding a peptide to amino-acid sequence via RNA + def translate_dna_to_peptide(dna_str): + """ Translate a DNA sequence encoding a peptide to amino-acid sequence via RNA. + + If 'N' is included in input dna, 'X' will be outputted since 'N' represents + uncertainty. Also will output a flag indicating if has stop codon. + + Parameters + ---------- + dna_str: str or List(str). dna string to be translated. + + Returns + ------- + aa_str: translated peptide + has_stop_codon: Indicator for showing if the input dna contains stop codon + + """ codontable = { 'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M', 'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T', @@ -118,7 +141,25 @@ def translate_dna_to_peptide(dna_str): def get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand): - if start_v2 != '.': + """ Get the mutated dna sub-sequence according to mutation specified by the variant_comb. + + Parameters + ---------- + background_seq: List(str). backgound sequence. + start_v1: int. start position of first vertex. + stop_v1: int. stop position of first vertex. + start_v2: int. start position of second vertex. + stop_v2: int. stop position of second vertex. + variant_comb: List(int). List of variant position. Like ['38', '43'] + mutation_sub_dic_maf: Dict. variant position -> variant details. + strand: gene strand + + Returns + ------- + final_dna: str. dna when applied somatic mutation. + + """ + if start_v2 != NOT_EXIST: if strand == '-': sub_dna_list = list(background_seq[start_v1:stop_v1][::-1] + background_seq[start_v2:stop_v2][::-1]) else: @@ -128,38 +169,63 @@ def get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, varian sub_dna_list = list(background_seq[start_v1:stop_v1][::-1]) else: sub_dna_list = list(background_seq[start_v1:stop_v1]) - if len(variant_comb) == 1: #no mutation exist + + if variant_comb == NOT_EXIST : # no mutation exist return ''.join(sub_dna_list) for variant_ipos in variant_comb: - ref_base = mutation_sub_dic_maf[variant_ipos]['ref_base'] mut_base = mutation_sub_dic_maf[variant_ipos]['mut_base'] - strand = mutation_sub_dic_maf[variant_ipos]['strand'] - variant_Classification = mutation_sub_dic_maf[variant_ipos]['variant_Classification'] - variant_Type = mutation_sub_dic_maf[variant_ipos]['variant_Type'] - sub_dna_list[variant_ipos-start_v1] = mut_base - return ''.join(sub_dna_list) + ref_base = mutation_sub_dic_maf[variant_ipos]['ref_base'] + # strand = mutation_sub_dic_maf[variant_ipos]['strand'] + # decide mutation happens in which exon vertice + # it may falls out of the two ranges due to readframe shift + if variant_ipos in range(start_v1, stop_v1): -def cross_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf, background_seq, peptide_accept_coord): - """ + if strand == '-': + pos = stop_v1-variant_ipos-1 + assert (sub_dna_list[pos] == ref_base) + sub_dna_list[pos] = mut_base + else: + pos = variant_ipos - start_v1 + assert (sub_dna_list[pos] == ref_base) + sub_dna_list[pos] = mut_base + + elif start_v2 != NOT_EXIST and variant_ipos in range(start_v2, stop_v2): + if strand == '-': + pos = stop_v2-variant_ipos+stop_v1-start_v1-1 + assert (sub_dna_list[pos] == ref_base) + sub_dna_list[pos] = mut_base + else: + pos = variant_ipos-start_v2+stop_v1-start_v1 + assert (sub_dna_list[pos] == ref_base) + sub_dna_list[pos] = mut_base + + final_dna = ''.join(sub_dna_list) + return final_dna + + +def cross_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf, ref_mut_seq, peptide_accept_coord): + """ Get translated peptide from the given exon pairs. Parameters ---------- - read_frame: tuple, (read_start_codon, read_stop_codon, emitting_frame) - strand: str, '+' or '-' - mut_seq: str, mutation string - background_seq: str, background string - peptide_accept_coord: np.ndarray, the 'next' vertex coordinate + read_frame: Tuple. (read_start_codon, read_stop_codon, emitting_frame) + strand: str. '+' or '-' + variant_comb: List(int). + mutation_sub_dic_maf: Dict. variant position -> variant details. + ref_mut_seq: Dict.['ref', 'background'] -> List(str) + peptide_accept_coord: The start and end position of next vertex. Positions of the first vertex + are already given in read_frame. Returns ------- - peptide_mut: str, the translated peptide of mutation sequence - peptide_ref: str, the translated peptide of reference sequence - start_v1, stop_v1: int, the corresponding start and end position of sequence of first exon which can output peptide - start_v2, stop_v2: - mut_has_stop_codon: bool, flag indicating if the sequence of interest has stop codon - is_single: bool, flag indicating if the outputed peptide only comes from one exon - next_reading_frame: tuple, the reading frame to be propagated to the next vertex + peptide: NamedTuple Peptide. has attribute ['ref', 'mut']. contain the output peptide + translated from reference sequence and mutated sequence. + coord: NamedTuple Coord. has attribute ['start_v1', 'stop_v1', 'start_v2', 'stop_v2'] + contains the true four position of exon pairs (after considering read framee) + that outputs the peptide. + flag: NamedTuple Flag. has attribute ['has_stop', 'is_isolated'] + next_reading_frame: Tuple. The reading frame to be propogated to the next vertex. """ cds_left_modi, cds_right_modi, emitting_frame = read_frame @@ -173,21 +239,25 @@ def cross_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf, # emitting_frame + accepting_frame = 3 accepting_frame = (3 - emitting_frame) % 3 - + if mutation_sub_dic_maf is None: + ref_seq = ref_mut_seq['ref'] + else: + ref_seq = ref_mut_seq['background'] # python is 0-based while gene annotation file(.gtf) is one based # so we need to do a little modification if strand == "+": start_v2 = peptide_accept_coord[0] stop_v2 = peptide_accept_coord[1] - next_emitting_frame - peptide_dna_str_mut = get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand) - peptide_dna_str_ref = background_seq[start_v1:stop_v1] + background_seq[start_v2:stop_v2] + peptide_dna_str_mut = get_sub_mut_dna(ref_mut_seq['background'], start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand) + peptide_dna_str_ref = ref_seq[start_v1:stop_v1] + ref_seq[start_v2:stop_v2] next_start_v1 = start_v2 + accepting_frame next_stop_v1 = peptide_accept_coord[1] else: # strand == "-" start_v2 = peptide_accept_coord[0] + next_emitting_frame stop_v2 = peptide_accept_coord[1] - peptide_dna_str_mut = complementary_seq(get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand)) - peptide_dna_str_ref = complementary_seq(background_seq[start_v1:stop_v1][::-1] + background_seq[start_v2:stop_v2][::-1]) + mut_seq = get_sub_mut_dna(ref_mut_seq['background'], start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand) + peptide_dna_str_mut = complementary_seq(mut_seq) + peptide_dna_str_ref = complementary_seq(ref_seq[start_v1:stop_v1][::-1] + ref_seq[start_v2:stop_v2][::-1]) next_start_v1 = peptide_accept_coord[0] next_stop_v1 = stop_v2 - accepting_frame @@ -202,48 +272,82 @@ def cross_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf, is_isolated = False if len(peptide_mut)*3 <= abs(stop_v1 - start_v1) + 1: is_isolated = True - - return peptide_mut, peptide_ref, start_v1, stop_v1, start_v2, stop_v2, \ - mut_has_stop_codon,is_isolated,next_reading_frame + jpos = 0.0 + else: + jpos = float(stop_v1 - start_v1) / 3.0 + peptide = Peptide(peptide_mut,peptide_ref) + coord = Coord(start_v1,stop_v1,start_v2,stop_v2) + flag = Flag(mut_has_stop_codon,is_isolated) + return peptide, coord, flag, next_reading_frame -def isolated_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf,background_seq): - """ - Deal with translating isolated cds, almost the same as cross_peptide_result +def isolated_peptide_result(read_frame, strand, variant_comb, mutation_sub_dic_maf, ref_mut_seq): + """ Deal with translating isolated cds, almost the same as cross_peptide_result Parameters ---------- - read_frame - strand - mut_seq - background_seq + read_frame: Tuple. (read_start_codon, read_stop_codon, emitting_frame) + strand: str. '+' or '-' + variant_comb: List(int). + mutation_sub_dic_maf: Dict. variant position -> variant details. + ref_mut_seq: Dict.['ref', 'background'] -> List(str) Returns ------- - is_isolated: Bool, True as Default - mut_has_stop_codon: Bool, assert to be True - start_v2, stop_v2: '-' means not exist + peptide: NamedTuple. has attribute ['ref', 'mut']. contain the output peptide + translated from reference sequence and mutated sequence. + coord: NamedTuple. has attribute ['start_v1', 'stop_v1', 'start_v2', 'stop_v2'] + contains the true two position of exon pairs (after considering read framee) + that outputs the peptide. 'start_v2', 'stop_v2' is set to be NOT_EXIST. + flag: NamedTuple. has attribute ['has_stop', 'is_isolated'] """ + Peptide = namedtuple('Peptide',['mut','ref']) + Coord = namedtuple('Coord',['start_v1','stop_v1','start_v2','stop_v2']) + Flag = namedtuple('Flag', ['has_stop', 'is_isolated']) + start_v1, stop_v1, emitting_frame = read_frame - start_v2 = '.' # does not exist - stop_v2 = '.' # does not exist + start_v2 = NOT_EXIST + stop_v2 = NOT_EXIST + + if mutation_sub_dic_maf is None: # no somatic mutation, the germline mutation will be the spotlight + ref_seq = ref_mut_seq['ref'] + else: + ref_seq = ref_mut_seq['background'] # we focus on somatic mutation in this case + mut_seq = ref_mut_seq['background'] + if strand == '+': - peptide_dna_str_mut = get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand) - peptide_dna_str_ref = background_seq[start_v1:stop_v1] + peptide_dna_str_mut = get_sub_mut_dna(mut_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand) + peptide_dna_str_ref = ref_seq[start_v1:stop_v1] else: - peptide_dna_str_mut = complementary_seq(get_sub_mut_dna(background_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand)) - peptide_dna_str_ref = background_seq[start_v1:stop_v1][::-1] + peptide_dna_str_mut = complementary_seq(get_sub_mut_dna(mut_seq, start_v1, stop_v1, start_v2, stop_v2, variant_comb, mutation_sub_dic_maf, strand)) + peptide_dna_str_ref = complementary_seq(ref_seq[start_v1:stop_v1][::-1]) peptide_mut, mut_has_stop_codon = translate_dna_to_peptide(peptide_dna_str_mut) peptide_ref, ref_has_stop_codon = translate_dna_to_peptide(peptide_dna_str_ref) is_isolated = True - return peptide_mut, peptide_ref, start_v1, stop_v1, start_v2, stop_v2, mut_has_stop_codon, is_isolated + peptide = Peptide(peptide_mut,peptide_ref) + coord = Coord(start_v1,stop_v1,start_v2,stop_v2) + flag = Flag(mut_has_stop_codon,is_isolated) + return peptide, coord, flag -def get_size_factor(strains,lib_file_path): + +def get_size_factor(strains, lib_file_path): + """ Get the expression adjustment parameter for certain samples. + + Parameters + ---------- + samples: List[str]. List of samples. + lib_file_path: str. libsize file path + + Returns + ------- + sf: 1darray. size factor. + + """ libs = sp.loadtxt(lib_file_path, dtype='str', skiprows=1, delimiter='\t') a, b = sp.where(strains[:, sp.newaxis] == libs[:, 0]) assert sp.all(libs[b, 0] == strains) @@ -252,7 +356,21 @@ def get_size_factor(strains,lib_file_path): sf = med / libs[:, 1].astype('float') return sf -def get_all_comb(array,r=None): + +def get_all_comb(array, r=None): + """ Get all the combination of items in the given array + Specifically used for generating variant combination + + Parameters + ---------- + array: 1D array. input array + r: int. The number of items in a combination + + Returns + ------- + result: List(Tuple). List of combination + + """ if r is None: r = len(array) result = [] @@ -260,27 +378,23 @@ def get_all_comb(array,r=None): result.extend(list(itertools.combinations(array,i))) return result + def is_mutation_within_exon_pair(pos_start,pos_end,mutation_pos): variant_pos = [pos for pos in mutation_pos] variant_pos_candi = [ipos for ipos in variant_pos if ipos > pos_start and ipos < pos_end] return variant_pos_candi - + + def is_isolated_cds(gene, idx): """ - If a vertex has a successor, it is not isolated. - - Generally if it has read frame, this read frame should be propogated by other - vertex. Therefore this vertex should not be isolated, except the very beginning - vertex, where the reading frame is assigned by gtf file. We mark all vertices that have - no incoming or outgoing edges as isolated. + Indicate if a peptide is translated by an isolated cds + Currently, it is a simple version. If the exon where the cds is + has no connected exon, it is isolated. (the method is not true in some cases) Parameters ---------- gene: gene object - idx: the id of vertex - - Returns - ------- + idx: exon id """ @@ -288,40 +402,117 @@ def is_isolated_cds(gene, idx): return False return sp.sum(gene.splicegraph.edges[:, idx]) == 0 - #sg = gene.splicegraph - ## AK TODO: this needs fixing. pop() will remove the reading frame, also it will pick an arbitrary one. - #coord_diff = sg.vertices[0, idx] - sg.reading_frames[idx].pop()[0] - #print(coord_diff) - #if abs(coord_diff) > 10: - # return True - -def is_output_redundant(gene, start_v1, stop_v1, start_v2, stop_v2): - strand = gene.strand - output_vertex_dict = gene.output_vertex_dict - if strand == '+': - if (stop_v1,start_v2) in output_vertex_dict: - all_output_comb = output_vertex_dict[(stop_v1,start_v2)] - for comb in all_output_comb: - if start_v1 >= comb[0] and stop_v2 <= comb[1]: - return True - output_vertex_dict[(stop_v1,start_v2)].append((start_v1,stop_v2)) - else: - output_vertex_dict[(stop_v1,start_v2)] = [(start_v1,stop_v2)] - else: # strand == '-' - if (start_v1, stop_v2) in output_vertex_dict: - all_output_comb = output_vertex_dict[(start_v1, stop_v2)] - for comb in all_output_comb: - if stop_v1 <= comb[0] and start_v2 >= comb[1]: - return True - output_vertex_dict[(start_v1, stop_v2)].append((stop_v1, start_v2)) - else: - output_vertex_dict[(start_v1, stop_v2)] = [(stop_v1, start_v2)] - return False -def is_in_junction_list(v1,v2,strand,junction_list): +def is_in_junction_list(v1,v2,strand,junction_list): + """Check if the intron is in concerned junction list""" return int(':'.join([str(v1[1]), str(v2[0]), strand]) in junction_list) - # coordi_match = np.logical_and(junction_list[:,0] == str(v1[1]),junction_list[:,1] == str(v2[0])) - # final_match = sum(np.logical_and(coordi_match,junction_list[:,2]==strand)) - # return final_match + +def get_exon_expr(gene,vstart,vstop,Segments,Idx): + """ Split the exon into segments and get the corresponding counts. + + Parameters + ---------- + gene: Object. Generated by SplAdder. + vstart: int. Start position of given exon. + vstop: int. Stop position of given exon. + Segments: Namedtuple, store segment expression information from count.hdf5. + has attribute ['expr', 'lookup_table']. + Idx: Namedtuple, has attribute idx.gene and idx.sample + + Returns + ------- + expr_list: List[Tuple(int,float)] (int, float) represents the length of segment + and the expression count of that segment. + + """ + if vstart == NOT_EXIST or vstop == NOT_EXIST: # isolated exon case + expr_list = [] + return expr_list + segments = gene.segmentgraph.segments + sv1_id = bisect.bisect(segments[0], vstart)-1 + sv2_id = bisect.bisect(segments[0], vstop)-1 + expr_list = [] + if sv1_id == sv2_id: + expr_list.append((vstop - vstart, Segments.expr[sv1_id, Idx.sample])) + else: + expr_list.append((segments[1, sv1_id] - vstart, Segments.expr[sv1_id,Idx.sample])) + for i in range(sv1_id + 1, sv2_id): + expr_list.append((segments[1, i] - segments[0, i], Segments.expr[i,Idx.sample])) + expr_list.append((vstop-segments[0, sv2_id], Segments.expr[sv2_id, Idx.sample])) + return expr_list + + +def get_segment_expr(gene, coord, Segments, Idx): + """ Get the segment expression for one exon-pair. + Apply 'get_exon_expr' for each exon and concatenate them. + + Parameters + ---------- + gene: Object. Generated by SplAdder. + coord: NamedTuple. has attribute ['start_v1', 'stop_v1', 'start_v2', 'stop_v2'] + contains the true four position of exon pairs (after considering read framee) + that outputs the peptide. + Segments: Namedtuple, store segment expression information from count.hdf5. + has attribute ['expr', 'lookup_table']. + Idx: Namedtuple, has attribute idx.gene and idx.sample + + Returns + ------- + mean_expr: float. The average expression counts for the given exon-pair + expr1: List[Tuple(int,float)] (int, float) represents the length of segment + and the expression count of that segment. + + """ + expr_list1 = get_exon_expr(gene,coord.start_v1,coord.stop_v1,Segments,Idx) + expr_list2 = get_exon_expr(gene,coord.start_v2,coord.stop_v2,Segments,Idx) + expr_list1.extend(expr_list2) + expr_sum = 0 + seg_len = 0 + for item in expr_list1: + expr_sum += item[0]*item[1] + seg_len += item[0] + mean_expr = int(expr_sum/seg_len) + return mean_expr + + +def get_idx(sample_idx_table, sample, gene_idx): + """ Create a aggregated Index with nametuple idx + Combine the gene_idx, sample_idx + + Parameters + ---------- + sample_idx_table: Dict. str -> int. Mapping sample to idx. + sample: str. sample name + gene_idx: int. Gene index, mainly for formatting the output. + + """ + if sample_idx_table is not None: + sample_idx = sample_idx_table[sample] + else: + sample_idx = None + idx = Idx(gene_idx,sample_idx) + return idx + + +def create_libsize(expr_distr_dict,output_fp): + """ create library_size text file. + + Calculate the 75% expression and sum of expression for each sample + and write into output_fp. + + Parameters + ---------- + expr_distr_dict: Dict. str -> List(float). Mapping sample to the expression of all exon pairs + output_fp: file pointer. library_size text + + """ + libsize_count = {sample:(np.percentile(expr_list,75),np.sum(expr_list)) for sample,expr_list in expr_distr_dict.items()} + with open(output_fp,'w') as f: + f.write('\t'.join(['sample','libsize_75percent','libsize_total_count'])+'\n') + for sample,count_tuple in libsize_count.items(): + line = '\t'.join([sample,str(round(count_tuple[0],1)),str(int(count_tuple[1]))])+'\n' + f.write(line) + + diff --git a/requirements.txt b/requirements.txt index fb83b1fe..216e3fba 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,5 @@ -# dependencies for 'silly_sum' example -pandas==0.22 -Click==6.0 +h5py==2.8.0 +numpy>=1.13 +psutil==5.4.6 +scipy==1.1.0 +biopython diff --git a/requirements_dev.txt b/requirements_dev.txt index 8a737e1e..ebf735fa 100644 --- a/requirements_dev.txt +++ b/requirements_dev.txt @@ -1,13 +1,16 @@ -pip==9.0.1 -bumpversion==0.5.3 -wheel==0.30.0 -watchdog==0.8.3 -flake8==3.5.0 -tox==2.9.1 -coverage==4.5.1 -Sphinx==1.7.0 -click==6.7 -pytest==3.4.1 -pytest-runner==2.11.1 -prospector==0.12.7 -vulture>=0.6,<0.25 # Required for https://github.com/landscapeio/prospector/issues/230 +pip>=9.0.1 +bumpversion>=0.5.3 +wheel>=0.30.0 +watchdog>=0.8.3 +flake8>=3.5.0 +tox>=2.9.1 +coverage>=4.5.1 +Sphinx>=1.7.0 +pytest>=3.4 +pytest-runner>=2.11.1 +prospector==0.12.8 +vulture>=0.6 +# TODO: this dependency is at the wrong place, should be in requirements.txt. +# However, then we get into issues with make install and tox. Will be fixed once +# spladder is in pypi +git+https://github.com/ratschlab/spladder.git@feature/simpleDeployment#subdirectory=python&egg=spladder-1.1.0 diff --git a/scripts/__init__.py b/scripts/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/immunopepper/apply_filter_criteria.py b/scripts/apply_filter_criteria.py similarity index 64% rename from immunopepper/apply_filter_criteria.py rename to scripts/apply_filter_criteria.py index edb0dc29..a11b4dc9 100644 --- a/immunopepper/apply_filter_criteria.py +++ b/scripts/apply_filter_criteria.py @@ -3,13 +3,25 @@ import scipy as sp import re -basedir = '/cluster/work/grlab/projects/coukos_immuno/results/output_peptide/ref' + +if len(sys.argv) < 2: + sys.stderr.write('Usage: %s \n' % sys.argv[0]) + sys.exit(1) +dataset = sys.argv[1] + +basedir = '/cluster/work/grlab/projects/coukos_immuno/results_%s/output_peptide/ref' % dataset filt_tag = '.filt' metafile = os.path.join(basedir, 'ref_metadata%s_REF.tsv.gz' % filt_tag) +metafile_gtex = os.path.join(basedir, 'ref_metadata%s_GTEX.tsv.gz' % filt_tag) fasta_file = os.path.join(basedir, 'ref_peptides%s.fa' % filt_tag) ### set filter criteria -celllines = ["OD5P", "EOC24", "MM12"] +if dataset == '20171031': + celllines = ["OD5P", "EOC24", "MM12", "EOC11", "MM33", "OMM475", "ONVC"] +elif dataset == '20180802': + celllines = ['C3N-02289', 'C3N-02671', 'EOC04', 'GY150806', 'JM-2', 'JM-4', 'MM170111', 'MM909362', 'MM909432', 'Me275', 'Me290', 'RCC14', 'RCC16', 'T1015A', 'T1185B'] +else: + celllines = [] filter_levels = ['1', '2', '3'] ### load metadata @@ -17,6 +29,11 @@ metaheader = metadata[0, :] metadata = metadata[1:, :] +### load metadata GTEX +metadata_gtex = sp.loadtxt(metafile_gtex, dtype='str' , delimiter='\t') +metaheader_gtex = metadata_gtex[0, :] +metadata_gtex = metadata_gtex[1:, :] + for cl in celllines: print('Processing %s' % cl) @@ -32,8 +49,10 @@ idx = sp.where(metaheader == 'junction_annotated')[0][0] k_idx3 = (metadata[:, idx].astype('int') > 0) ### non-gtex junction - idx = sp.where(metaheader == 'is_in_junction_list')[0][0] - k_idx4 = (metadata[:, idx].astype('int') == 0) + #idx = sp.where(metaheader == 'is_in_junction_list')[0][0] + #k_idx4 = (metadata[:, idx].astype('int') == 0) + gt_idx = sp.where([_.startswith('junc_exp:gtex') for _ in metaheader_gtex])[0] + k_idx4 = (metadata_gtex[:, gt_idx].astype('float').max(axis=1) < 3) idx = sp.where(metaheader == 'output_id')[0][0] diff --git a/scripts/create_bam_file.py b/scripts/create_bam_file.py new file mode 100644 index 00000000..5ed9a1b1 --- /dev/null +++ b/scripts/create_bam_file.py @@ -0,0 +1,186 @@ +from immunopepper.immuno_preprocess import preprocess_ann +from immunopepper.utils import complementary_seq +import numpy as np +import os +from collections import Counter + +# steps to add new transcript +# 1. modify test1pos.gtf file +# 2. modify create_test_genome file to make tailor-made gene +# 3. delete quick_test_data/spladder +# 4. create new splicegraph with command tools +# 4. run main_immuno.py +def create_test_genome(L,stop_position,data_dir,seed=1): + np.random.seed(seed) + number_list = np.random.randint(0,4,L) + map_dict = {0:'A', 1:'G', 2:'C', 3:'T'} + dna_list = [map_dict[i] for i in number_list] + for pos in stop_position: + dna_list[pos:pos+3] = 'TAG' + + # modify + dna_list[69] = 'C' # remove stop codon + dna_list[98] = 'G' # remove stop codon + dna_list[39] = 'T' # create stop codon in mutation mode + + # create GT/AG for splicing site + dna_list[25] = 'G' # in case the dna_list[24:27] = 'TAG' + dna_list[26:28] = 'GT' + dna_list[29:31] = 'GT' + dna_list[36:38] = 'AG' + dna_list[50:52] = 'GT' + dna_list[59:61] = 'AG' + dna_list[64:66] = 'AG' + dna_list[75:77] = 'GT' + dna_list[85:87] = 'AG' + + pos_dna = ''.join(dna_list) + neg_dna = complementary_seq(pos_dna[::-1]) + pos_seq_file = os.path.join(data_dir,'test1pos.fa') + neg_seq_file = os.path.join(data_dir,'test1neg.fa') + f_pos = open(pos_seq_file, 'w') + f_neg = open(neg_seq_file, 'w') + f_pos.write('>X dna:chromosome chromosome:GRCh37:X:1:155270560:1'+'\n') + f_pos.write(pos_dna) + f_pos.close() + f_neg.write('>X dna:chromosome chromosome:GRCh37:1:1:155270560:1'+'\n') + f_neg.write(neg_dna) + f_neg.close() + return pos_dna + + +def create_full_from_pos(data_dir, L): + posgtf_file = os.path.join(data_dir, 'test1pos.gtf') + posmaf_file = os.path.join(data_dir, 'test1pos.maf') + posvcf_file = os.path.join(data_dir, 'test1pos.vcf') + neggtf_file = os.path.join(data_dir, 'test1neg.gtf') + negmaf_file = os.path.join(data_dir, 'test1neg.maf') + negvcf_file = os.path.join(data_dir, 'test1neg.vcf') + + f = open(posgtf_file, 'r') + lines = f.readlines() + new_line_list = [] + for line in lines: + item = line.split('\t') + start_pos = L+1-int(item[3]) + end_pos = L+1-int(item[4]) + #new_detail = item[8].replace('GENE1', 'GENE2') + #new_detail = new_detail.replace('TRANS1', 'TRANS2') + item[3] = str(end_pos) + item[4] = str(start_pos) + item[6] = '-' + new_line = '\t'.join(item) + new_line_list.append(new_line) + f = open(neggtf_file,'w') + f.writelines(new_line_list) + f.close() + + f = open(posmaf_file, 'r') + lines = f.readlines() + new_line_list = [lines[0]] + for line in lines[1:]: + item = line.split('\t') + pos = item[5] + ref_base = item[10] + mut_base = item[12] + sample = item[15] + neg_pre_base = complementary_seq(ref_base) + neg_new_base = complementary_seq(mut_base) + new_sample = sample.replace('pos', 'neg') + new_pos = L+1-int(pos) + item[5] = str(new_pos) + item[6] = str(new_pos) + item[7] = '-' + item[10] = neg_pre_base + item[11], item[12] = neg_pre_base, neg_new_base + item[15], item[16] = new_sample, new_sample + new_line = '\t'.join(item) + new_line_list.append(new_line) + f = open(negmaf_file,'w') + f.writelines(new_line_list) + f.close() + + f = open(posvcf_file, 'r') + lines = f.readlines() + new_line_list = lines[:29] + headline = lines[29].replace('pos','neg') + new_line_list.extend(headline) + for line in lines[30:]: + item = line.split('\t') + pos = item[1] + ref_base = item[3] + mut_base = item[4] + neg_pre_base = complementary_seq(ref_base) + neg_new_base = complementary_seq(mut_base) + neg_pos = L+1-int(pos) + item[1] = str(neg_pos) + item[3] = neg_pre_base + item[4] = neg_new_base + new_line = '\t'.join(item) + new_line_list.extend(new_line) + f = open(negvcf_file,'w') + f.writelines(new_line_list) + f.close() + + +def create_bam_file(data_dir, seed=1): + np.random.seed(seed) + posref_path = os.path.join(data_dir, 'test1pos.fa') + with open(posref_path, 'r') as fpos: + posref_seq = fpos.readlines()[1] + posann_path = os.path.join(data_dir, 'test1pos.gtf') + pos_genetable = preprocess_ann(posann_path) + + expr = [10, 0, 25, 15, 10] + reads_L = 15 + cover = 100 + + expr_file = os.path.join(data_dir, 'expr_ts.txt') + f_expr = open(expr_file, 'w') + total_reads_list = [] + ts_dict = {} + expr_list = [] + for i, key_value_pair in enumerate(pos_genetable.ts_to_cds.items()): + ts_name = key_value_pair[0] + pos_exon_coord = key_value_pair[1] + ts = '' + for coord_pair in pos_exon_coord: + start_pos = coord_pair[0] + read_frame = coord_pair[2] + stop_pos = coord_pair[1] + ts += posref_seq[start_pos+read_frame:stop_pos+1] + N = expr[i]*cover + pos = np.random.randint(0,len(ts)-reads_L,N) + pos_counter = Counter(pos) + expr_arr = np.zeros(len(ts)) + expr_list.append(expr_arr) + ts_dict[ts_name] = ts + for ipos in pos_counter.keys(): + expr_arr[ipos:ipos+reads_L] += pos_counter[ipos] + expr_arr = [str(int(i_expr)) for i_expr in expr_arr] + new_line = ts_name+'\t'+'\t'.join(expr_arr)+'\n' + f_expr.write(new_line) + reads_list = [ts[ipos:ipos+reads_L] for ipos in pos] + total_reads_list.extend(reads_list) + f_expr.close() + output_dir = os.path.join(data_dir, 'test1_1.fq') + f = open(output_dir, 'w') + total_num = len(total_reads_list) + for i in range(total_num-1, -1, -1): + line1 = '@test1_' + str((i+1)*2) + '/1'+'\n' + f.write(line1) + line2 = total_reads_list[i]+'\n' + f.write(line2) + line3 = '+\n' + f.write(line3) + line4 = reads_L*'G'+'\n' + f.write(line4) + + +data_dir = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/test1/data' +create_test_genome(150, [73, 102], data_dir) +print("Successfully create test genome") +create_full_from_pos(data_dir, 150) +print("Successfully create gtf, maf and vcf file") +create_bam_file(data_dir) +print("Successfully create bam segments") diff --git a/scripts/generate_gt_file.py b/scripts/generate_gt_file.py new file mode 100644 index 00000000..5548f96e --- /dev/null +++ b/scripts/generate_gt_file.py @@ -0,0 +1,83 @@ +import os +import gzip +pos_result_path = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/test1/test1neg' +neg_esult_path = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/test1/test1pos' + +def rename_as_gt_file(result_path): + file_list = os.listdir(result_path) + for file in file_list: + item = file.split('.') + suffix = item[-1] + if suffix == 'gz': + file_path = os.path.join(result_path, file) + lines = gzip.open(file_path,'rb') + new_file_name = item[0]+'_gt.tsv' + new_file_path = os.path.join(result_path,new_file_name) + with open(new_file_path, 'w') as ftsv: + ftsv.writelines(lines.read()) + else: # fa file + name = item[0] + name_part = name.split('_') + if name_part[-1] != 'gt': + name_part.append('gt') + new_name = '_'.join(name_part)+'.'+suffix + file_path = os.path.join(result_path,file) + new_file_path = os.path.join(result_path,new_name) + os.rename(file_path,new_file_path) +rename_as_gt_file(pos_result_path) +rename_as_gt_file(neg_esult_path) + +# split the groundtruth to positive and negative part +# def change_neg_gene_id(neg_lines,mode='tsv'): +# new_neg_lines = [] +# if mode == 'tsv': +# for line in neg_lines: +# items = line.split('\t') +# id_items = items[0].split('.') +# id_items[0] = '0' +# new_id = '.'.join(id_items) +# items[0] = new_id +# new_neg_lines.append('\t'.join(items)) +# if mode == 'fa': +# for i, line in enumerate(neg_lines): +# if i%2 != 0: +# line_list = list(line) +# line_list[1] = '0' +# new_line = ''.join(line_list) +# new_neg_lines.append(new_line) +# else: +# new_neg_lines.append(line) +# return new_neg_lines +# +# for file in file_list: +# item = file.split('.') +# suffix = item[1] +# name = item[0] +# new_posname = name+'_pos'+'.'+suffix +# new_negname = name+'_neg'+'.'+suffix +# pos_path = os.path.join(result_path,new_posname) +# neg_path = os.path.join(result_path,new_negname) +# ori_path = os.path.join(result_path,file) +# with open(pos_path,'w') as fpos, open(neg_path,'w') as fneg, open(ori_path,'r') as fori: +# lines = fori.readlines() +# if suffix == 'tsv': +# assert ((len(lines) - 1) % 2 == 0) +# mid = (len(lines) + 1) / 2 +# new_poslines = lines[0]+''.join(lines[1:mid]) +# neg_lines = change_neg_gene_id(lines[mid:],'tsv') +# new_neglines = lines[0]+''.join(neg_lines) +# fpos.writelines(new_poslines) +# fneg.writelines(new_neglines) +# else: +# assert(len(lines)%2 == 0) +# mid = len(lines)/2 +# new_poslines = lines[:mid] +# new_neglines = change_neg_gene_id(lines[mid:], 'fa') +# fpos.writelines(new_poslines) +# fneg.writelines(new_neglines) +# fpos.close() +# fneg.close() + + + + diff --git a/scripts/validate_count.py b/scripts/validate_count.py new file mode 100644 index 00000000..f2d0c6b6 --- /dev/null +++ b/scripts/validate_count.py @@ -0,0 +1,158 @@ +import numpy as np +import cPickle +import h5py +expr_path = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/data/expr_ts.txt' +splicegraph_path = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle' +count_path = '/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper/tests/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5' + +count = h5py.File(count_path) +f = open(splicegraph_path,'r') +gene,metadata = cPickle.load(f) +gene0 = gene[0] + +with open(expr_path,'r') as f: + lines = f.readlines() + expr_dict = {} + for line in lines: + item = line.split('\t') + trans = item[0] + expr = [int(iexpr) for iexpr in item[1:]] + expr_dict[trans] = expr + +expr1 = expr_dict['TRANS1.1'] +expr3 = expr_dict['TRANS1.3'] +expr4 = expr_dict['TRANS1.4'] +expr5 = expr_dict['TRANS1.5'] +expr2 = expr_dict['TRANS1.2'] + + +# segment1 [4,26) +# trans1 (11,28,0),(38,49,0),(61,72,0) +# trans2 (60,74,0),(87,101,0) +# trans3 (11,28,1),(38,41,0) -> (12,28,0),(38,42) +# trans4 (14,25,2),(38,49,0),(66,74,0),(87,101,0) -> (16,25,0) +# trans5 (53,83,0) + +dna = 'GTAATGTGTAAGATGACGCACGCATGGTGGTATTGGAGATGGGTTGCGGAGTAAGTTCGAGTTCAGGTACGTATAGTTGCTAAGTAGTCGACGTTCTGGTGGTAGACCTTTTGTTACCCAATTGGGTAAGGCAGCCATGTTGATATACAT' + +ts_dict = {'TRANS1.1': 'GATGACGCACGCATGGTGATGGGTTGCGGATTCAGGTACGTA', + 'TRANS1.2': 'GTTCAGGTACGTATATCGACGTTCTGGTGG', + 'TRANS1.3': 'ATGACGCACGCATGGTGATGG', + 'TRANS1.4': 'CGCACGCATGATGGGTTGCGGAGTACGTATATCGACGTTCTGGTGG', + 'TRANS1.5': 'AGTTCGAGTTCAGGTACGTATAGTTGCTAAG'} + +ts_to_cds={'TRANS1.1': [(11, 28, 0), (38, 49, 0), (61, 72, 0)], + 'TRANS1.2': [(60, 74, 0), (87, 101, 0)], + 'TRANS1.3': [(11, 28, 1), (38, 41, 0)], + 'TRANS1.4': [(14, 25, 2), (38, 49, 0), (66, 74, 0), (87, 101, 0)], + 'TRANS1.5': [(53, 83, 0)]} + +# segment1 [4,26), 1287.2 = 1287.2 +segment1 = np.zeros(26-4) +segment1[11-4:26-4] += expr1[:26-11] +segment1[12-4:26-4] += expr3[:25-11] +segment1[16-4:25-4] += expr4[:23-14] +assert np.mean(segment1) == count['segments'][0] + +# segment2 [26,29), # 2606 != 2528 +segment2 = np.zeros(29-26) +assert(dna[26:29] == ts_dict['TRANS1.1'][15:18]) +segment2 += expr1[26-11:29-11] +assert(dna[26:29] == ts_dict['TRANS1.3'][14:17]) +segment2 += expr3[26-12:29-12] +print(np.mean(segment2)) + +# segment3 [38,49), 1495 != 1409.9 +segment3 = np.zeros(49-38) +segment3 += expr1[18:29] +assert(dna[38:49] == ts_dict['TRANS1.1'][18:29]) +segment3 += expr4[10:21] +assert(dna[38:49] == ts_dict['TRANS1.4'][10:21]) +segment3[:4] += expr3[17:] +assert(dna[38:42] == ts_dict['TRANS1.3'][17:]) +print(np.mean(segment3)) + +# segment4 [49,50) 1115 = 1115 +segment4 = 0 +assert(dna[49] == ts_dict['TRANS1.1'][29]) +assert(dna[49] == ts_dict['TRANS1.4'][21]) +segment4 += expr1[29] +segment4 += expr4[21] +print(np.mean(segment4)) + +# segment5 [50,53) 0 = 0 + +# segment6 [53,61) 297.15 = 297.15 +segment = np.zeros(61-53) +assert(dna[53:61] == ts_dict['TRANS1.5'][:61-53]) +assert(dna[60] == ts_dict['TRANS1.2'][0]) +segment += expr5[:8] +segment[-1] += expr2[0] +print(np.mean(segment)) + +# segment7 [61,66) 1814 != 1763 +segment = np.zeros(66-61) +assert(dna[61:66] == ts_dict['TRANS1.1'][-12:-7]) +assert(dna[61:66] == ts_dict['TRANS1.2'][1:6]) +assert(dna[61:66] == ts_dict['TRANS1.5'][8:13]) +segment += expr1[-12:-7] +segment += expr2[1:6] +segment += expr5[8:13] +print(np.mean(segment)) + +# segment8 [66,75) 787 != 1717 +segment = np.zeros(75-66) +#assert(dna[66:75] == ts_dict['TRANS1.4'][1:6]) +assert(dna[66:75] == ts_dict['TRANS1.5'][13:22]) +#segment += expr4[1:6] +segment += expr5[13:22] +print(np.mean(segment)) + + +# segment9 [75,84) 244 = 244 +assert(dna[75:84] == ts_dict['TRANS1.5'][22:]) +print(np.mean(expr5[22:])) + +# segment10 [84,87), 0 = 0 + +# segment11 [87,90) 874 != 807 +segment = np.zeros(90-87) +assert(dna[89] == ts_dict['TRANS1.4'][-13]) +assert(dna[87:90] == ts_dict['TRANS1.2'][15:18]) +segment[-1] += expr4[-13] +segment += expr2[15:18] +print(np.mean(segment)) + +# segment12 [90,102) 363 = 363 +segment = np.zeros(102-90) +assert(dna[90:101] == ts_dict['TRANS1.4'][-12:-1]) +assert(dna[90:101] == ts_dict['TRANS1.2'][18:29]) +segment[:-1] += expr4[-12:-1] +segment[:-1] += expr2[18:29] +print(np.mean(segment)) + + + +def get_relative_id(vstart,v_stop,v_pair_list): + pass + +def get_expected_expression(vstart, vstop, expr_dict, ts_dict, dna, ts_to_cds): + for trans_name,trans_comp in enumerate(ts_to_cds.items()): + read_frame = trans_comp[0][2] + v_list = [] + for pair in trans_comp: + pair_start = pair[0]+ read_frame + pair_end = pair[1] + read_frame + v_list.extend(list(set(range(vstart,vstop)).intersection(set(range(pair_start,pair_end))))) + v_max = max(v_list) + v_min = min(v_list) + id = get_relative_id(v_min,v_max,trans_comp) + + + +for idx in range(gene0.segmentgraph.segments.shape[1]): + vstart = gene0.segmentgraph.segments[0,idx] + vstop = gene0.segmentgraph.segments[1,idx] + expe_expr = get_expected_expression(vstart,vstop,expr_dict,ts_dict,ts_to_cds) + assert(int(count['segments'][idx]) == int(expe_expr)) + diff --git a/setup.cfg b/setup.cfg index a84d588b..b74bde39 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.0 +current_version = 1.0.0 commit = True tag = True @@ -18,10 +18,8 @@ universal = 1 exclude = docs [aliases] -# Define setup.py command aliases here test = pytest [tool:pytest] collect_ignore = ['setup.py'] - diff --git a/setup.py b/setup.py index 99171dd1..49079352 100644 --- a/setup.py +++ b/setup.py @@ -31,10 +31,8 @@ 'Programming Language :: Python :: 3.6', ], description="Software to translate splicing graphs into peptides", - entry_points={ - 'console_scripts': [ - 'silly_sum=immunopepper.silly_sum:main', - ], + entry_points = { + 'console_scripts': ['immunopepper=immunopepper.main_immuno:cmd_entry'], }, install_requires=requirements, license="MIT license", @@ -47,6 +45,6 @@ test_suite='tests', tests_require=test_requirements, url='https://github.com/ratschlab/immunopepper', - version='0.1.0', + version='1.0.0', zip_safe=False, ) diff --git a/step.sh b/step.sh new file mode 100755 index 00000000..c784b95f --- /dev/null +++ b/step.sh @@ -0,0 +1,59 @@ +#!/bin/bash + +set -e + +work_dir="/Users/jiayu/PycharmProjects/CBM_RA/projects2018_immunopepper" +spladder_dir="/Users/jiayu/PycharmProjects/CBM_RA/spladder/python" +testname='test1' + +script_dir=${work_dir}/scripts +test_data_dir=${work_dir}/tests/$testname + + +# Step 1and2: make changes on the test1.gtf file and reference sequence +# make some changes on the expression data and Create fq file +#python ${script_dir}/create_bam_file.py + +# Step 3: Generating genome indexes for STAR +#mkdir -p ${test_data_dir}/data/genome/pos || TRUE +#mkdir -p ${test_data_dir}/data/genome/neg || TRUE +#STAR --runThreadN 3 --runMode genomeGenerate --genomeDir ${test_data_dir}/data/genome/pos --genomeFastaFiles ${test_data_dir}/data/test1pos.fa --sjdbGTFfile ${test_data_dir}/data/test1pos.gtf --sjdbOverhang 14 --sjdbInsertSave Basic +#STAR --runThreadN 3 --runMode genomeGenerate --genomeDir ${test_data_dir}/data/genome/neg --genomeFastaFiles ${test_data_dir}/data/test1neg.fa --sjdbGTFfile ${test_data_dir}/data/test1neg.gtf --sjdbOverhang 14 --sjdbInsertSave Basic + + +## Step 4: Running maping jobs +#mkdir ${test_data_dir}/data/align || TRUE +#STAR --runThreadN 3 --genomeDir ${test_data_dir}/data/genome/pos --readFilesIn ${test_data_dir}/data/test1_1.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${test_data_dir}/data/align/pos +#STAR --runThreadN 3 --genomeDir ${test_data_dir}/data/genome/neg --readFilesIn ${test_data_dir}/data/test1_1.fq --outSAMtype BAM SortedByCoordinate --outFileNamePrefix ${test_data_dir}/data/align/neg + +# Step 5: Rename the bam file so that we can control the strain id +#mv ${test_data_dir}/data/align/posAligned.sortedByCoord.out.bam ${test_data_dir}/data/align/test1pos.bam || TRUE +#mv ${test_data_dir}/data/align/negAligned.sortedByCoord.out.bam ${test_data_dir}/data/align/test1neg.bam || TRUE + +## Step 6: Using Samtools to create bai file +#samtools index ${test_data_dir}/data/align/test1pos.bam +#samtools index ${test_data_dir}/data/align/test1neg.bam + +## Step 7: Generating splicegraph and corresponding count file using spladder +#rm ${test_data_dir}/data/test1pos.gtf.pickle || TRUE +#rm ${test_data_dir}/data/test1neg.gtf.pickle || TRUE +#rm -rf ${test_data_dir}/data/posgraph || TRUE +#rm -rf ${test_data_dir}/data/neggraph || TRUE +#python ${spladder_dir}/spladder.py --insert_ir=n --insert_es=n --insert_ni=n --remove_se=n --validate_sg=n -b ${test_data_dir}/data/align/test1pos.bam -o ${test_data_dir}/data/posgraph -a ${test_data_dir}/data/test1pos.gtf -v y -c 3 -M merge_graphs -T n -P n -p n -q y +#python ${spladder_dir}/spladder.py --insert_ir=n --insert_es=n --insert_ni=n --remove_se=n --validate_sg=n -b ${test_data_dir}/data/align/test1neg.bam -o ${test_data_dir}/data/neggraph -a ${test_data_dir}/data/test1neg.gtf -v y -c 3 -M merge_graphs -T n -P n -p n -q y + +## Step8: run main file to generate ground result +# positive case +python ${script_dir}/main_immuno.py --mutation_mode ref --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1pos.gtf --splice_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1pos.fa --count_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1pos --debug --vcf_path ${test_data_dir}/data/test1pos.vcf --maf_path ${test_data_dir}/data/test1pos.maf +python ${script_dir}/main_immuno.py --mutation_mode somatic --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1pos.gtf --splice_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1pos.fa --count_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1pos --debug --vcf_path ${test_data_dir}/data/test1pos.vcf --maf_path ${test_data_dir}/data/test1pos.maf +python ${script_dir}/main_immuno.py --mutation_mode germline --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1pos.gtf --splice_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1pos.fa --count_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1pos --debug --vcf_path ${test_data_dir}/data/test1pos.vcf --maf_path ${test_data_dir}/data/test1pos.maf +python ${script_dir}/main_immuno.py --mutation_mode somatic_and_germline --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1pos.gtf --splice_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1pos.fa --count_path ${test_data_dir}/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1pos --debug --vcf_path ${test_data_dir}/data/test1pos.vcf --maf_path ${test_data_dir}/data/test1pos.maf + +# negative case +python ${script_dir}/main_immuno.py --mutation_mode ref --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1neg.gtf --splice_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1neg.fa --count_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1neg --debug --vcf_path ${test_data_dir}/data/test1neg.vcf --maf_path ${test_data_dir}/data/test1neg.maf +python ${script_dir}/main_immuno.py --mutation_mode somatic --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1neg.gtf --splice_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1neg.fa --count_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1neg --debug --vcf_path ${test_data_dir}/data/test1neg.vcf --maf_path ${test_data_dir}/data/test1neg.maf +python ${script_dir}/main_immuno.py --mutation_mode germline --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1neg.gtf --splice_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1neg.fa --count_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1neg --debug --vcf_path ${test_data_dir}/data/test1neg.vcf --maf_path ${test_data_dir}/data/test1neg.maf +python ${script_dir}/main_immuno.py --mutation_mode somatic_and_germline --output_dir ${test_data_dir} --ann_path ${test_data_dir}/data/test1neg.gtf --splice_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle --ref_path ${test_data_dir}/data/test1neg.fa --count_path ${test_data_dir}/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 --samples test1neg --debug --vcf_path ${test_data_dir}/data/test1neg.vcf --maf_path ${test_data_dir}/data/test1neg.maf + +# step9: unzip gz file and rename to _gt file +python ${script_dir}/generate_gt_file.py diff --git a/tests/data/chrx.maf b/tests/data/chrx.maf deleted file mode 100644 index 80bdb49b..00000000 --- a/tests/data/chrx.maf +++ /dev/null @@ -1,3 +0,0 @@ -Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER COSMIC CENTERS CONTEXT DBVS NCALLERS -JAKMIP3 0 . GRCh37 3 50197088 50197088 + Silent SNP C C T rs763531628 . OMM475.T OMM475.N C C . . . . . . . . . . . . . . . c.2169C>T p.%3D p.D723D ENST00000298622 18/24 82 16 65 123 123 0 JAKMIP3,synonymous_variant,p.%3D,ENST00000298622,;JAKMIP3,non_coding_transcript_exon_variant,,ENST00000477275,; T ENSG00000188385 ENST00000298622 Transcript synonymous_variant 2307 2169 723 D gaC/gaT rs763531628,COSM2148890 . . 1 JAKMIP3 HGNC 23523 protein_coding YES CCDS44494.1 ENSP00000298622 JKIP3_HUMAN . UPI000157482F . . . 18/24 . hmmpanther:PTHR18935:SF5,hmmpanther:PTHR18935 . . . . . . . . . . 0,1 . . . . . LOW . SNV . . 0,1 . . . . . . . . . . PASS NONE MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS CTGGACGAGGA byFrequency 5 -PANX3 0 . GRCh37 3 50197090 50197090 + Missense_Mutation SNP G G A . . OMM475.T OMM475.N G G . . . . . . . . . . . . . . . c.887G>A p.Arg296Gln p.R296Q ENST00000284288 4/4 217 127 89 188 188 0 PANX3,missense_variant,p.Arg296Gln,ENST00000284288,;TBRG1,upstream_gene_variant,,ENST00000531667,;TBRG1,upstream_gene_variant,,ENST00000375005,;TBRG1,upstream_gene_variant,,ENST00000441174,;TBRG1,upstream_gene_variant,,ENST00000529543,;TBRG1,upstream_gene_variant,,ENST00000284290,;TBRG1,upstream_gene_variant,,ENST00000452080,;TBRG1,upstream_gene_variant,,ENST00000530731,;TBRG1,upstream_gene_variant,,ENST00000473629,; A ENSG00000154143 ENST00000284288 Transcript missense_variant 954 887 296 R/Q cGg/cAg COSM211013 . . 1 PANX3 HGNC 20573 protein_coding YES CCDS8447.1 ENSP00000284288 PANX3_HUMAN . UPI0000131264 . tolerated(0.37) benign(0.001) 4/4 . hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF3,PROSITE_profiles:PS51013 . . . . . . . . . . 1 . . . . . MODERATE . SNV . . 1 . . . . . . . . . . PASS SITE|p.R296Q|c.887G>A|3 MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS ATGTCGGTGGG . 5 \ No newline at end of file diff --git a/tests/data/example.gff b/tests/data/example.gff deleted file mode 100644 index 4b7121d3..00000000 --- a/tests/data/example.gff +++ /dev/null @@ -1,10 +0,0 @@ -1 example gene 1 100 . + . ID=gene1;Note=protein_coding_gene;Name=gene1 -1 example mRNA 1 58 . + . ID=gene1.1;Parent=gene1;Name=gene1.1;Index=1 -1 example exon 10 18 . + . Parent=gene1.1 -1 example five_prime_UTR 10 12 . + . Parent=gene1.1 -1 example CDS 13 18 . + 0 Parent=gene1.1 -1 example exon 30 38 . + . Parent=gene1.1 -1 example CDS 30 38 . + 1 Parent=gene1.1 -1 example exon 50 58 . + . Parent=gene1.1 -1 example CDS 50 52 . + 0 Parent=gene1.1 -1 example three_prime_UTR 53 58 . + . Parent=gene1.1 diff --git a/tests/data/example.gff.pickle b/tests/data/example.gff.pickle deleted file mode 100644 index dd28657c..00000000 Binary files a/tests/data/example.gff.pickle and /dev/null differ diff --git a/tests/data/numbers.txt b/tests/data/numbers.txt deleted file mode 100644 index c6c82e85..00000000 --- a/tests/data/numbers.txt +++ /dev/null @@ -1,5 +0,0 @@ -1.0 --1.2 -0.9999 -3.3 -45.9 diff --git a/tests/test1/data/align/test1neg.bam b/tests/test1/data/align/test1neg.bam new file mode 100644 index 00000000..4be071a0 Binary files /dev/null and b/tests/test1/data/align/test1neg.bam differ diff --git a/tests/test1/data/align/test1neg.bam.bai b/tests/test1/data/align/test1neg.bam.bai new file mode 100644 index 00000000..d633cdad Binary files /dev/null and b/tests/test1/data/align/test1neg.bam.bai differ diff --git a/tests/test1/data/align/test1pos.bam b/tests/test1/data/align/test1pos.bam new file mode 100644 index 00000000..371612a2 Binary files /dev/null and b/tests/test1/data/align/test1pos.bam differ diff --git a/tests/test1/data/align/test1pos.bam.bai b/tests/test1/data/align/test1pos.bam.bai new file mode 100644 index 00000000..bebc90fc Binary files /dev/null and b/tests/test1/data/align/test1pos.bam.bai differ diff --git a/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 b/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 new file mode 100644 index 00000000..3887e8db Binary files /dev/null and b/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 differ diff --git a/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle b/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle new file mode 100644 index 00000000..1ce8467a Binary files /dev/null and b/tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle differ diff --git a/tests/test1/data/neggraph/spladder/genes_graph_conf3.test1neg.pickle b/tests/test1/data/neggraph/spladder/genes_graph_conf3.test1neg.pickle new file mode 100644 index 00000000..e918c1fa Binary files /dev/null and b/tests/test1/data/neggraph/spladder/genes_graph_conf3.test1neg.pickle differ diff --git a/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 b/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 new file mode 100644 index 00000000..ea25f4f1 Binary files /dev/null and b/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5 differ diff --git a/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle b/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle new file mode 100644 index 00000000..82ac261b Binary files /dev/null and b/tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle differ diff --git a/tests/test1/data/posgraph/spladder/genes_graph_conf3.test1pos.pickle b/tests/test1/data/posgraph/spladder/genes_graph_conf3.test1pos.pickle new file mode 100644 index 00000000..bfef30ca Binary files /dev/null and b/tests/test1/data/posgraph/spladder/genes_graph_conf3.test1pos.pickle differ diff --git a/tests/test1/data/small.gencode.v19.gff b/tests/test1/data/small.gencode.v19.gff new file mode 100644 index 00000000..0c1fdc81 --- /dev/null +++ b/tests/test1/data/small.gencode.v19.gff @@ -0,0 +1,156 @@ +##gff-version 3 +# /cbio/grlab/share/software/cufflinks/cufflinks-2.2.1.Linux_x86_64/gffread -o gencode.v19.annotation.hs37d5_chr.gff -F -O gencode.v19.annotation.hs37d5_chr.gtf +1 HAVANA transcript 11869 14409 . + . ID=ENST00000456328.2;geneID=ENSG00000223972.4;gene_name=DDX11L1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_transcript;transcript_status=KNOWN;level=2;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1;Name=DDX11L1-002 +1 HAVANA exon 11869 12227 . + . Parent=ENST00000456328.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_transcript;transcript_status=KNOWN;transcript_name=DDX11L1-002;level=2;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +1 HAVANA exon 12613 12721 . + . Parent=ENST00000456328.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_transcript;transcript_status=KNOWN;transcript_name=DDX11L1-002;level=2;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +1 HAVANA exon 13221 14409 . + . Parent=ENST00000456328.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_transcript;transcript_status=KNOWN;transcript_name=DDX11L1-002;level=2;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +1 HAVANA gene 11869 14412 . + . ID=ENSG00000223972.4;geneID=ENSG00000223972.4;gene_name=DDX11L1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=pseudogene;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000000961.2;Name=DDX11L1 +1 HAVANA gene 11869 14412 . + . Parent=ENSG00000223972.4 +1 ENSEMBL transcript 11872 14412 . + . ID=ENST00000515242.2;geneID=ENSG00000223972.4;gene_name=DDX11L1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000961.2;Name=DDX11L1-201 +1 ENSEMBL exon 11872 12227 . + . Parent=ENST00000515242.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-201;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL exon 12613 12721 . + . Parent=ENST00000515242.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-201;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL exon 13225 14412 . + . Parent=ENST00000515242.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-201;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL transcript 11874 14409 . + . ID=ENST00000518655.2;geneID=ENSG00000223972.4;gene_name=DDX11L1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000961.2;Name=DDX11L1-202 +1 ENSEMBL exon 11874 12227 . + . Parent=ENST00000518655.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-202;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL exon 12595 12721 . + . Parent=ENST00000518655.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-202;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL exon 13403 13655 . + . Parent=ENST00000518655.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-202;level=3;havana_gene=OTTHUMG00000000961.2 +1 ENSEMBL exon 13661 14409 . + . Parent=ENST00000518655.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-202;level=3;havana_gene=OTTHUMG00000000961.2 +1 HAVANA transcript 12010 13670 . + . ID=ENST00000450305.2;geneID=ENSG00000223972.4;gene_name=DDX11L1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2;Name=DDX11L1-001 +1 HAVANA exon 12010 12057 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 HAVANA exon 12179 12227 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 HAVANA exon 12613 12697 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 HAVANA exon 12975 13052 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 HAVANA exon 13221 13374 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 HAVANA exon 13453 13670 . + . Parent=ENST00000450305.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=transcribed_unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=DDX11L1-001;level=2;ont=PGO:0000019;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +1 ENSEMBL transcript 14363 24886 . - . ID=ENST00000541675.1;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000958.1;Name=WASH7P-204 +1 ENSEMBL exon 14363 14829 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 14970 15038 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16854 17055 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17233 17364 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17498 17504 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17606 17742 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17915 18061 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 18268 18369 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 24734 24886 . - . Parent=ENST00000541675.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-204;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL transcript 14363 29370 . - . ID=ENST00000423562.1;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000958.1;Name=WASH7P-201 +1 ENSEMBL exon 14363 14829 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 14970 15038 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15796 15947 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16607 16765 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16858 17055 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17233 17368 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17606 17742 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17915 18061 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 24738 24891 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 29321 29370 . - . Parent=ENST00000423562.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-201;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL transcript 14363 29370 . - . ID=ENST00000438504.2;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000958.1;Name=WASH7P-202 +1 ENSEMBL exon 14363 14829 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 14970 15038 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15796 15901 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15904 15947 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16607 16765 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16854 17055 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17233 17364 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17602 17742 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17915 18061 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 18268 18379 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 24738 24891 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 29321 29370 . - . Parent=ENST00000438504.2;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-202;level=3;havana_gene=OTTHUMG00000000958.1 +1 HAVANA gene 14363 29806 . - . ID=ENSG00000227232.4;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=pseudogene;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000000958.1;Name=WASH7P +1 HAVANA gene 14363 29806 . - . Parent=ENSG00000227232.4 +1 HAVANA transcript 14404 29570 . - . ID=ENST00000488147.1;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1;Name=WASH7P-001 +1 HAVANA exon 14404 14501 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 15005 15038 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 15796 15947 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 16607 16765 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 16858 17055 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 17233 17368 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 17606 17742 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 17915 18061 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 18268 18366 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 24738 24891 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 HAVANA exon 29534 29570 . - . Parent=ENST00000488147.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +1 ENSEMBL transcript 14411 29806 . - . ID=ENST00000538476.1;geneID=ENSG00000227232.4;gene_name=WASH7P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000000958.1;Name=WASH7P-203 +1 ENSEMBL exon 14411 14502 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15000 15038 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15796 15901 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 15904 15947 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16607 16745 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16748 16765 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 16858 17055 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17233 17364 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17602 17742 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 17915 18061 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 18268 18366 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 24737 24891 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 ENSEMBL exon 29534 29806 . - . Parent=ENST00000538476.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=WASH7P-203;level=3;havana_gene=OTTHUMG00000000958.1 +1 HAVANA transcript 29554 31097 . + . ID=ENST00000473358.1;geneID=ENSG00000243485.2;gene_name=MIR1302-11;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1;Name=MIR1302-11-001 +1 HAVANA exon 29554 30039 . + . Parent=ENST00000473358.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-001;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +1 HAVANA exon 30564 30667 . + . Parent=ENST00000473358.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-001;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +1 HAVANA exon 30976 31097 . + . Parent=ENST00000473358.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-001;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +1 HAVANA gene 29554 31109 . + . ID=ENSG00000243485.2;geneID=ENSG00000243485.2;gene_name=MIR1302-11;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=NOVEL;level=2;havana_gene=OTTHUMG00000000959.2;Name=MIR1302-11 +1 HAVANA gene 29554 31109 . + . Parent=ENSG00000243485.2 +1 HAVANA transcript 30267 31109 . + . ID=ENST00000469289.1;geneID=ENSG00000243485.2;gene_name=MIR1302-11;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2;Name=MIR1302-11-002 +1 HAVANA exon 30267 30667 . + . Parent=ENST00000469289.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-002;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2 +1 HAVANA exon 30976 31109 . + . Parent=ENST00000469289.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-002;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2 +1 ENSEMBL transcript 30366 30503 . + . ID=ENST00000607096.1;geneID=ENSG00000243485.2;gene_name=MIR1302-11;gene_type=lincRNA;gene_status=NOVEL;transcript_type=miRNA;transcript_status=KNOWN;level=3;tag=basic;havana_gene=OTTHUMG00000000959.2;Name=MIR1302-11-201 +1 ENSEMBL exon 30366 30503 . + . Parent=ENST00000607096.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=miRNA;transcript_status=KNOWN;transcript_name=MIR1302-11-201;level=3;tag=basic;havana_gene=OTTHUMG00000000959.2 +1 HAVANA gene 34554 36081 . - . ID=ENSG00000237613.2;geneID=ENSG00000237613.2;gene_name=FAM138A;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000000960.1;Name=FAM138A +1 HAVANA gene 34554 36081 . - . Parent=ENSG00000237613.2 +1 HAVANA transcript 34554 36081 . - . ID=ENST00000417324.1;geneID=ENSG00000237613.2;gene_name=FAM138A;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1;Name=FAM138A-001 +1 HAVANA exon 34554 35174 . - . Parent=ENST00000417324.1;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=FAM138A-001;level=2;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +1 HAVANA exon 35277 35481 . - . Parent=ENST00000417324.1;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=FAM138A-001;level=2;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +1 HAVANA exon 35721 36081 . - . Parent=ENST00000417324.1;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=FAM138A-001;level=2;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +1 HAVANA transcript 35245 36073 . - . ID=ENST00000461467.1;geneID=ENSG00000237613.2;gene_name=FAM138A;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1;Name=FAM138A-002 +1 HAVANA exon 35245 35481 . - . Parent=ENST00000461467.1;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=FAM138A-002;level=2;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1 +1 HAVANA exon 35721 36073 . - . Parent=ENST00000461467.1;gene_type=lincRNA;gene_status=KNOWN;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=FAM138A-002;level=2;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1 +1 HAVANA transcript 52473 53312 . + . ID=ENST00000606857.1;geneID=ENSG00000268020.2;gene_name=OR4G4P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000185779.1;havana_transcript=OTTHUMT00000471235.1;Name=OR4G4P-001 +1 HAVANA exon 52473 53312 . + . Parent=ENST00000606857.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=OR4G4P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000185779.1;havana_transcript=OTTHUMT00000471235.1 +1 HAVANA gene 52473 54936 . + . ID=ENSG00000268020.2;geneID=ENSG00000268020.2;gene_name=OR4G4P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=pseudogene;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000185779.1;Name=OR4G4P +1 HAVANA gene 52473 54936 . + . Parent=ENSG00000268020.2 +1 ENSEMBL transcript 53049 54936 . + . ID=ENST00000594647.1;geneID=ENSG00000268020.2;gene_name=OR4G4P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=3;havana_gene=OTTHUMG00000185779.1;Name=OR4G4P-201 +1 ENSEMBL exon 53049 53067 . + . Parent=ENST00000594647.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=OR4G4P-201;level=3;havana_gene=OTTHUMG00000185779.1 +1 ENSEMBL exon 54830 54936 . + . Parent=ENST00000594647.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=OR4G4P-201;level=3;havana_gene=OTTHUMG00000185779.1 +1 HAVANA gene 62948 63887 . + . ID=ENSG00000240361.1;geneID=ENSG00000240361.1;gene_name=OR4G11P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=pseudogene;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000001095.2;Name=OR4G11P +1 HAVANA gene 62948 63887 . + . Parent=ENSG00000240361.1 +1 HAVANA transcript 62948 63887 . + . ID=ENST00000492842.1;geneID=ENSG00000240361.1;gene_name=OR4G11P;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000001095.2;havana_transcript=OTTHUMT00000003224.2;Name=OR4G11P-001 +1 HAVANA exon 62948 63887 . + . Parent=ENST00000492842.1;gene_type=pseudogene;gene_status=KNOWN;transcript_type=unprocessed_pseudogene;transcript_status=KNOWN;transcript_name=OR4G11P-001;level=2;ont=PGO:0000005;havana_gene=OTTHUMG00000001095.2;havana_transcript=OTTHUMT00000003224.2 +1 HAVANA gene 69091 70008 . + . ID=ENSG00000186092.4;geneID=ENSG00000186092.4;gene_name=OR4F5;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000001094.1;Name=OR4F5 +1 HAVANA gene 69091 70008 . + . Parent=ENSG00000186092.4 +1 HAVANA mRNA 69091 70008 . + . ID=ENST00000335137.3;geneID=ENSG00000186092.4;gene_name=OR4F5;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;level=2;tag=CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.1;havana_transcript=OTTHUMT00000003223.1;Name=OR4F5-001 +1 HAVANA exon 69091 70008 . + . Parent=ENST00000335137.3;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;transcript_name=OR4F5-001;level=2;tag=CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.1;havana_transcript=OTTHUMT00000003223.1 +1 HAVANA CDS 69091 70006 . + 0 Parent=ENST00000335137.3 +1 HAVANA transcript 89295 120932 . - . ID=ENST00000466430.1;geneID=ENSG00000238009.2;gene_name=RP11-34P13.7;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=basic;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003225.1;Name=RP11-34P13.7-001 +1 HAVANA exon 89295 91629 . - . Parent=ENST00000466430.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-001;level=2;tag=basic;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003225.1 +1 HAVANA exon 92091 92240 . - . Parent=ENST00000466430.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-001;level=2;tag=basic;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003225.1 +1 HAVANA exon 112700 112804 . - . Parent=ENST00000466430.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-001;level=2;tag=basic;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003225.1 +1 HAVANA exon 120775 120932 . - . Parent=ENST00000466430.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-001;level=2;tag=basic;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003225.1 +1 HAVANA gene 89295 133566 . - . ID=ENSG00000238009.2;geneID=ENSG00000238009.2;gene_name=RP11-34P13.7;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=NOVEL;level=2;havana_gene=OTTHUMG00000001096.2;Name=RP11-34P13.7 +1 HAVANA gene 89295 133566 . - . Parent=ENSG00000238009.2 +1 HAVANA gene 89551 91105 . - . ID=ENSG00000239945.1;geneID=ENSG00000239945.1;gene_name=RP11-34P13.8;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=NOVEL;level=2;havana_gene=OTTHUMG00000001097.2;Name=RP11-34P13.8 +1 HAVANA gene 89551 91105 . - . Parent=ENSG00000239945.1 +1 HAVANA transcript 89551 91105 . - . ID=ENST00000495576.1;geneID=ENSG00000239945.1;gene_name=RP11-34P13.8;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=basic;havana_gene=OTTHUMG00000001097.2;havana_transcript=OTTHUMT00000003226.2;Name=RP11-34P13.8-001 +1 HAVANA exon 89551 90050 . - . Parent=ENST00000495576.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.8-001;level=2;tag=basic;havana_gene=OTTHUMG00000001097.2;havana_transcript=OTTHUMT00000003226.2 +1 HAVANA exon 90287 91105 . - . Parent=ENST00000495576.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.8-001;level=2;tag=basic;havana_gene=OTTHUMG00000001097.2;havana_transcript=OTTHUMT00000003226.2 +1 HAVANA transcript 92230 129217 . - . ID=ENST00000477740.1;geneID=ENSG00000238009.2;gene_name=RP11-34P13.7;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003688.1;Name=RP11-34P13.7-003 +1 HAVANA exon 92230 92240 . - . Parent=ENST00000477740.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-003;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003688.1 +1 HAVANA exon 112700 112804 . - . Parent=ENST00000477740.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-003;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003688.1 +1 HAVANA exon 120721 120932 . - . Parent=ENST00000477740.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-003;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003688.1 +1 HAVANA exon 129055 129217 . - . Parent=ENST00000477740.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-003;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003688.1 +1 HAVANA transcript 110953 129173 . - . ID=ENST00000471248.1;geneID=ENSG00000238009.2;gene_name=RP11-34P13.7;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003687.1;Name=RP11-34P13.7-002 +1 HAVANA exon 110953 111357 . - . Parent=ENST00000471248.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-002;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003687.1 +1 HAVANA exon 112700 112804 . - . Parent=ENST00000471248.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-002;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003687.1 +1 HAVANA exon 129055 129173 . - . Parent=ENST00000471248.1;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-002;level=2;tag=not_best_in_genome_evidence;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003687.1 +1 HAVANA transcript 129081 133566 . - . ID=ENST00000453576.2;geneID=ENSG00000238009.2;gene_name=RP11-34P13.7;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;level=2;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003689.1;Name=RP11-34P13.7-004 +1 HAVANA exon 129081 129223 . - . Parent=ENST00000453576.2;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-004;level=2;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003689.1 +1 HAVANA exon 133374 133566 . - . Parent=ENST00000453576.2;gene_type=lincRNA;gene_status=NOVEL;transcript_type=lincRNA;transcript_status=KNOWN;transcript_name=RP11-34P13.7-004;level=2;havana_gene=OTTHUMG00000001096.2;havana_transcript=OTTHUMT00000003689.1 +1 HAVANA gene 131025 134836 . + . ID=ENSG00000233750.3;geneID=ENSG00000233750.3;gene_name=CICP27;gene_type=pseudogene;gene_status=KNOWN;transcript_type=pseudogene;transcript_status=KNOWN;level=1;tag=pseudo_consens;havana_gene=OTTHUMG00000001257.3;Name=CICP27 +1 HAVANA gene 131025 134836 . + . Parent=ENSG00000233750.3 +1 HAVANA transcript 131025 134836 . + . ID=ENST00000442987.3;geneID=ENSG00000233750.3;gene_name=CICP27;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_pseudogene;transcript_status=KNOWN;level=1;ont=PGO:0000004;tag=pseudo_consens;havana_gene=OTTHUMG00000001257.3;havana_transcript=OTTHUMT00000003691.3;Name=CICP27-001 +1 HAVANA exon 131025 134836 . + . Parent=ENST00000442987.3;gene_type=pseudogene;gene_status=KNOWN;transcript_type=processed_pseudogene;transcript_status=KNOWN;transcript_name=CICP27-001;level=1;ont=PGO:0000004;tag=pseudo_consens;havana_gene=OTTHUMG00000001257.3;havana_transcript=OTTHUMT00000003691.3 +1 ENSEMBL gene 134901 139379 . - . ID=ENSG00000237683.5;geneID=ENSG00000237683.5;gene_name=AL627309.1;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;level=3;Name=AL627309.1 +1 ENSEMBL gene 134901 139379 . - . Parent=ENSG00000237683.5 +1 ENSEMBL mRNA 134901 139379 . - . ID=ENST00000423372.3;geneID=ENSG00000237683.5;gene_name=AL627309.1;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;level=3;tag=appris_principal;Name=AL627309.1-201 +1 ENSEMBL exon 134901 135802 . - . Parent=ENST00000423372.3;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;transcript_name=AL627309.1-201;level=3;tag=appris_principal +1 ENSEMBL exon 137621 139379 . - . Parent=ENST00000423372.3;gene_type=protein_coding;gene_status=KNOWN;transcript_type=protein_coding;transcript_status=KNOWN;transcript_name=AL627309.1-201;level=3;tag=appris_principal +1 ENSEMBL CDS 138533 139309 . - 0 Parent=ENST00000423372.3 diff --git a/tests/test1/data/small.gencode.v19.gtf b/tests/test1/data/small.gencode.v19.gtf new file mode 100644 index 00000000..9963d809 --- /dev/null +++ b/tests/test1/data/small.gencode.v19.gtf @@ -0,0 +1,155 @@ +##description: evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74) +##provider: GENCODE +##contact: gencode@sanger.ac.uk +##format: gtf +##date: 2013-12-05 +chr1 HAVANA gene 11869 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENSG00000223972.4"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; +chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000456328.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_status "KNOWN"; transcript_name "DDX11L1-002"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 ENSEMBL transcript 11872 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 11872 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00002234632.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 12613 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00003608237.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 13225 14412 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000515242.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-201"; exon_number 3; exon_id "ENSE00002306041.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL transcript 11874 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 11874 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002269724.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 12595 12721 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00002270865.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 13403 13655 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002216795.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 ENSEMBL exon 13661 14409 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000518655.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-202"; exon_number 4; exon_id "ENSE00002303382.1"; level 3; havana_gene "OTTHUMG00000000961.2"; +chr1 HAVANA transcript 12010 13670 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12010 12057 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12179 12227 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12613 12697 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12975 13052 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 13221 13374 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 5; exon_id "ENSE00001746346.2"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 13453 13670 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 6; exon_id "ENSE00001863096.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA gene 14363 29806 . - . gene_id "ENSG00000227232.4"; transcript_id "ENSG00000227232.4"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P"; level 2; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL transcript 14363 29370 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 29321 29370 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 1; exon_id "ENSE00001718035.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 24738 24891 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 2; exon_id "ENSE00003624050.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 18268 18379 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 3; exon_id "ENSE00001642865.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17915 18061 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 4; exon_id "ENSE00003638984.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17602 17742 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 5; exon_id "ENSE00001699689.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17233 17364 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 6; exon_id "ENSE00001656010.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16854 17055 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 7; exon_id "ENSE00001760358.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16607 16765 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 8; exon_id "ENSE00003618297.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15904 15947 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 9; exon_id "ENSE00001375216.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15796 15901 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 10; exon_id "ENSE00001388009.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14970 15038 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 11; exon_id "ENSE00003497546.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14363 14829 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000438504.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-202"; exon_number 12; exon_id "ENSE00003511598.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL transcript 14363 24886 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 24734 24886 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 1; exon_id "ENSE00002254515.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 18268 18369 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 2; exon_id "ENSE00002303227.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17915 18061 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 3; exon_id "ENSE00003638984.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17606 17742 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 4; exon_id "ENSE00003629019.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17498 17504 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 5; exon_id "ENSE00002285713.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17233 17364 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 6; exon_id "ENSE00001656010.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16854 17055 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 7; exon_id "ENSE00001760358.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14970 15038 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 8; exon_id "ENSE00003497546.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14363 14829 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000541675.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-204"; exon_number 9; exon_id "ENSE00003511598.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL transcript 14363 29370 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 29321 29370 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 1; exon_id "ENSE00001718035.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 24738 24891 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 2; exon_id "ENSE00003603734.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17915 18061 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 3; exon_id "ENSE00003513603.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17606 17742 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 4; exon_id "ENSE00003565315.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17233 17368 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 5; exon_id "ENSE00003685767.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16858 17055 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 6; exon_id "ENSE00003553898.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16607 16765 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 7; exon_id "ENSE00003621279.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15796 15947 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 8; exon_id "ENSE00002030414.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14970 15038 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 9; exon_id "ENSE00003591210.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14363 14829 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000423562.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-201"; exon_number 10; exon_id "ENSE00003693168.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 HAVANA transcript 14404 29570 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 29534 29570 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 1; exon_id "ENSE00001890219.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 24738 24891 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 2; exon_id "ENSE00003507205.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 18268 18366 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 3; exon_id "ENSE00003477500.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17915 18061 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 4; exon_id "ENSE00003565697.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17606 17742 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 5; exon_id "ENSE00003475637.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17233 17368 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 6; exon_id "ENSE00003502542.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 16858 17055 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 7; exon_id "ENSE00003553898.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 16607 16765 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 8; exon_id "ENSE00003621279.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 15796 15947 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 9; exon_id "ENSE00002030414.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 15005 15038 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 10; exon_id "ENSE00001935574.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 14404 14501 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000488147.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-001"; exon_number 11; exon_id "ENSE00001843071.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 ENSEMBL transcript 14411 29806 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 29534 29806 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 1; exon_id "ENSE00001378845.2"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 24737 24891 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 2; exon_id "ENSE00002317443.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 18268 18366 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 3; exon_id "ENSE00003682243.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17915 18061 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 4; exon_id "ENSE00003638984.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17602 17742 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 5; exon_id "ENSE00001699689.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 17233 17364 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 6; exon_id "ENSE00001656010.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16858 17055 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 7; exon_id "ENSE00003632482.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16748 16765 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 8; exon_id "ENSE00002275850.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 16607 16745 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 9; exon_id "ENSE00002241734.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15904 15947 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 10; exon_id "ENSE00001375216.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15796 15901 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 11; exon_id "ENSE00001388009.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 15000 15038 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 12; exon_id "ENSE00002215305.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 ENSEMBL exon 14411 14502 . - . gene_id "ENSG00000227232.4"; transcript_id "ENST00000538476.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "WASH7P-203"; exon_number 13; exon_id "ENSE00002295553.1"; level 3; havana_gene "OTTHUMG00000000958.1"; +chr1 HAVANA gene 29554 31109 . + . gene_id "ENSG00000243485.2"; transcript_id "ENSG00000243485.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "MIR1302-11"; level 2; havana_gene "OTTHUMG00000000959.2"; +chr1 HAVANA transcript 29554 31097 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-001"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 29554 30039 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-001"; exon_number 1; exon_id "ENSE00001947070.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 30564 30667 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-001"; exon_number 2; exon_id "ENSE00001922571.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 30976 31097 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-001"; exon_number 3; exon_id "ENSE00001827679.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA transcript 30267 31109 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-002"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 HAVANA exon 30267 30667 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-002"; exon_number 1; exon_id "ENSE00001841699.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 HAVANA exon 30976 31109 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-002"; exon_number 2; exon_id "ENSE00001890064.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 ENSEMBL transcript 30366 30503 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000607096.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "miRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-201"; level 3; tag "basic"; havana_gene "OTTHUMG00000000959.2"; +chr1 ENSEMBL exon 30366 30503 . + . gene_id "ENSG00000243485.2"; transcript_id "ENST00000607096.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "MIR1302-11"; transcript_type "miRNA"; transcript_status "KNOWN"; transcript_name "MIR1302-11-201"; exon_number 1; exon_id "ENSE00003695741.1"; level 3; tag "basic"; havana_gene "OTTHUMG00000000959.2"; +chr1 HAVANA gene 34554 36081 . - . gene_id "ENSG00000237613.2"; transcript_id "ENSG00000237613.2"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A"; level 2; havana_gene "OTTHUMG00000000960.1"; +chr1 HAVANA transcript 34554 36081 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-001"; level 2; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 35721 36081 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-001"; exon_number 1; exon_id "ENSE00001656588.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 35277 35481 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-001"; exon_number 2; exon_id "ENSE00001669267.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 34554 35174 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-001"; exon_number 3; exon_id "ENSE00001727627.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA transcript 35245 36073 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-002"; level 2; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA exon 35721 36073 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-002"; exon_number 1; exon_id "ENSE00001618781.2"; level 2; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA exon 35245 35481 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_status "KNOWN"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "FAM138A-002"; exon_number 2; exon_id "ENSE00001874421.1"; level 2; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA gene 52473 54936 . + . gene_id "ENSG00000268020.2"; transcript_id "ENSG00000268020.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P"; level 2; havana_gene "OTTHUMG00000185779.1"; +chr1 HAVANA transcript 52473 53312 . + . gene_id "ENSG00000268020.2"; transcript_id "ENST00000606857.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P-001"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000185779.1"; havana_transcript "OTTHUMT00000471235.1"; +chr1 HAVANA exon 52473 53312 . + . gene_id "ENSG00000268020.2"; transcript_id "ENST00000606857.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P-001"; exon_number 1; exon_id "ENSE00003698237.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000185779.1"; havana_transcript "OTTHUMT00000471235.1"; +chr1 ENSEMBL transcript 53049 54936 . + . gene_id "ENSG00000268020.2"; transcript_id "ENST00000594647.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P-201"; level 3; havana_gene "OTTHUMG00000185779.1"; +chr1 ENSEMBL exon 53049 53067 . + . gene_id "ENSG00000268020.2"; transcript_id "ENST00000594647.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P-201"; exon_number 1; exon_id "ENSE00003076518.1"; level 3; havana_gene "OTTHUMG00000185779.1"; +chr1 ENSEMBL exon 54830 54936 . + . gene_id "ENSG00000268020.2"; transcript_id "ENST00000594647.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G4P-201"; exon_number 2; exon_id "ENSE00003074125.1"; level 3; havana_gene "OTTHUMG00000185779.1"; +chr1 HAVANA gene 62948 63887 . + . gene_id "ENSG00000240361.1"; transcript_id "ENSG00000240361.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G11P"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G11P"; level 2; havana_gene "OTTHUMG00000001095.2"; +chr1 HAVANA transcript 62948 63887 . + . gene_id "ENSG00000240361.1"; transcript_id "ENST00000492842.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G11P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G11P-001"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000001095.2"; havana_transcript "OTTHUMT00000003224.2"; +chr1 HAVANA exon 62948 63887 . + . gene_id "ENSG00000240361.1"; transcript_id "ENST00000492842.1"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "OR4G11P"; transcript_type "unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "OR4G11P-001"; exon_number 1; exon_id "ENSE00001830178.1"; level 2; ont "PGO:0000005"; havana_gene "OTTHUMG00000001095.2"; havana_transcript "OTTHUMT00000003224.2"; +chr1 HAVANA gene 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENSG00000186092.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5"; level 2; havana_gene "OTTHUMG00000001094.1"; +chr1 HAVANA transcript 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA exon 69091 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA CDS 69091 70005 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA start_codon 69091 69093 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA stop_codon 70006 70008 . + 0 gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1; exon_id "ENSE00002319515.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA UTR 70006 70008 . + . gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1"; +chr1 HAVANA gene 89295 133566 . - . gene_id "ENSG00000238009.2"; transcript_id "ENSG00000238009.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "RP11-34P13.7"; level 2; havana_gene "OTTHUMG00000001096.2"; +chr1 HAVANA transcript 89295 120932 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000466430.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-001"; level 2; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003225.1"; +chr1 HAVANA exon 120775 120932 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000466430.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-001"; exon_number 1; exon_id "ENSE00001606755.2"; level 2; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003225.1"; +chr1 HAVANA exon 112700 112804 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000466430.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-001"; exon_number 2; exon_id "ENSE00001957285.1"; level 2; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003225.1"; +chr1 HAVANA exon 92091 92240 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000466430.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-001"; exon_number 3; exon_id "ENSE00001944529.1"; level 2; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003225.1"; +chr1 HAVANA exon 89295 91629 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000466430.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-001"; exon_number 4; exon_id "ENSE00001846804.1"; level 2; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003225.1"; +chr1 HAVANA transcript 92230 129217 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000477740.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-003"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003688.1"; +chr1 HAVANA exon 129055 129217 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000477740.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-003"; exon_number 1; exon_id "ENSE00001919246.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003688.1"; +chr1 HAVANA exon 120721 120932 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000477740.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-003"; exon_number 2; exon_id "ENSE00001171005.3"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003688.1"; +chr1 HAVANA exon 112700 112804 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000477740.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-003"; exon_number 3; exon_id "ENSE00001957285.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003688.1"; +chr1 HAVANA exon 92230 92240 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000477740.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-003"; exon_number 4; exon_id "ENSE00001896976.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003688.1"; +chr1 HAVANA transcript 110953 129173 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000471248.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-002"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003687.1"; +chr1 HAVANA exon 129055 129173 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000471248.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-002"; exon_number 1; exon_id "ENSE00001934975.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003687.1"; +chr1 HAVANA exon 112700 112804 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000471248.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-002"; exon_number 2; exon_id "ENSE00001957285.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003687.1"; +chr1 HAVANA exon 110953 111357 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000471248.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-002"; exon_number 3; exon_id "ENSE00001879696.1"; level 2; tag "not_best_in_genome_evidence"; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003687.1"; +chr1 HAVANA transcript 129081 133566 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000453576.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-004"; level 2; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003689.1"; +chr1 HAVANA exon 133374 133566 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000453576.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-004"; exon_number 1; exon_id "ENSE00001737600.2"; level 2; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003689.1"; +chr1 HAVANA exon 129081 129223 . - . gene_id "ENSG00000238009.2"; transcript_id "ENST00000453576.2"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.7"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.7-004"; exon_number 2; exon_id "ENSE00001827073.1"; level 2; havana_gene "OTTHUMG00000001096.2"; havana_transcript "OTTHUMT00000003689.1"; +chr1 HAVANA gene 89551 91105 . - . gene_id "ENSG00000239945.1"; transcript_id "ENSG00000239945.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.8"; transcript_type "lincRNA"; transcript_status "NOVEL"; transcript_name "RP11-34P13.8"; level 2; havana_gene "OTTHUMG00000001097.2"; +chr1 HAVANA transcript 89551 91105 . - . gene_id "ENSG00000239945.1"; transcript_id "ENST00000495576.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.8-001"; level 2; tag "basic"; havana_gene "OTTHUMG00000001097.2"; havana_transcript "OTTHUMT00000003226.2"; +chr1 HAVANA exon 90287 91105 . - . gene_id "ENSG00000239945.1"; transcript_id "ENST00000495576.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.8-001"; exon_number 1; exon_id "ENSE00001907785.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000001097.2"; havana_transcript "OTTHUMT00000003226.2"; +chr1 HAVANA exon 89551 90050 . - . gene_id "ENSG00000239945.1"; transcript_id "ENST00000495576.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-34P13.8"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-34P13.8-001"; exon_number 2; exon_id "ENSE00001927725.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000001097.2"; havana_transcript "OTTHUMT00000003226.2"; +chr1 HAVANA gene 131025 134836 . + . gene_id "ENSG00000233750.3"; transcript_id "ENSG00000233750.3"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "CICP27"; transcript_type "pseudogene"; transcript_status "KNOWN"; transcript_name "CICP27"; level 1; tag "pseudo_consens"; havana_gene "OTTHUMG00000001257.3"; +chr1 HAVANA transcript 131025 134836 . + . gene_id "ENSG00000233750.3"; transcript_id "ENST00000442987.3"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "CICP27"; transcript_type "processed_pseudogene"; transcript_status "KNOWN"; transcript_name "CICP27-001"; level 1; ont "PGO:0000004"; tag "pseudo_consens"; havana_gene "OTTHUMG00000001257.3"; havana_transcript "OTTHUMT00000003691.3"; +chr1 HAVANA exon 131025 134836 . + . gene_id "ENSG00000233750.3"; transcript_id "ENST00000442987.3"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "CICP27"; transcript_type "processed_pseudogene"; transcript_status "KNOWN"; transcript_name "CICP27-001"; exon_number 1; exon_id "ENSE00001625118.3"; level 1; ont "PGO:0000004"; tag "pseudo_consens"; havana_gene "OTTHUMG00000001257.3"; havana_transcript "OTTHUMT00000003691.3"; +chr1 ENSEMBL gene 134901 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENSG00000237683.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1"; level 3; +chr1 ENSEMBL transcript 134901 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL exon 137621 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL CDS 138533 139309 . - 0 gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL stop_codon 138530 138532 . - 0 gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 1; exon_id "ENSE00002221580.1"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL exon 134901 135802 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; exon_number 2; exon_id "ENSE00002314092.1"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL UTR 137621 138532 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL UTR 139310 139379 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; +chr1 ENSEMBL UTR 134901 135802 . - . gene_id "ENSG00000237683.5"; transcript_id "ENST00000423372.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "AL627309.1"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "AL627309.1-201"; level 3; tag "basic"; tag "appris_principal"; diff --git a/tests/test1/data/small.gencode.v29.gff3 b/tests/test1/data/small.gencode.v29.gff3 new file mode 100644 index 00000000..d44cc580 --- /dev/null +++ b/tests/test1/data/small.gencode.v29.gff3 @@ -0,0 +1,83 @@ +##gff-version 3 +#description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94) +#provider: GENCODE +#contact: gencode-help@ebi.ac.uk +#format: gff3 +#date: 2018-08-30 +##sequence-region chr1 1 248956422 +chr1 HAVANA gene 11869 14409 . + . ID=ENSG00000223972.5;gene_id=ENSG00000223972.5;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;level=2;havana_gene=OTTHUMG00000000961.2 +chr1 HAVANA transcript 11869 14409 . + . ID=ENST00000456328.2;Parent=ENSG00000223972.5;gene_id=ENSG00000223972.5;transcript_id=ENST00000456328.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=processed_transcript;transcript_name=DDX11L1-202;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +chr1 HAVANA exon 11869 12227 . + . ID=exon:ENST00000456328.2:1;Parent=ENST00000456328.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000456328.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=processed_transcript;transcript_name=DDX11L1-202;exon_number=1;exon_id=ENSE00002234944.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +chr1 HAVANA exon 12613 12721 . + . ID=exon:ENST00000456328.2:2;Parent=ENST00000456328.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000456328.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=processed_transcript;transcript_name=DDX11L1-202;exon_number=2;exon_id=ENSE00003582793.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +chr1 HAVANA exon 13221 14409 . + . ID=exon:ENST00000456328.2:3;Parent=ENST00000456328.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000456328.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=processed_transcript;transcript_name=DDX11L1-202;exon_number=3;exon_id=ENSE00002312635.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000362751.1 +chr1 HAVANA transcript 12010 13670 . + . ID=ENST00000450305.2;Parent=ENSG00000223972.5;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 12010 12057 . + . ID=exon:ENST00000450305.2:1;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=1;exon_id=ENSE00001948541.1;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 12179 12227 . + . ID=exon:ENST00000450305.2:2;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=2;exon_id=ENSE00001671638.2;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 12613 12697 . + . ID=exon:ENST00000450305.2:3;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=3;exon_id=ENSE00001758273.2;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 12975 13052 . + . ID=exon:ENST00000450305.2:4;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=4;exon_id=ENSE00001799933.2;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 13221 13374 . + . ID=exon:ENST00000450305.2:5;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=5;exon_id=ENSE00001746346.2;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA exon 13453 13670 . + . ID=exon:ENST00000450305.2:6;Parent=ENST00000450305.2;gene_id=ENSG00000223972.5;transcript_id=ENST00000450305.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=DDX11L1;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=DDX11L1-201;exon_number=6;exon_id=ENSE00001863096.1;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000000961.2;havana_transcript=OTTHUMT00000002844.2 +chr1 HAVANA gene 14404 29570 . - . ID=ENSG00000227232.5;gene_id=ENSG00000227232.5;gene_type=unprocessed_pseudogene;gene_name=WASH7P;level=2;havana_gene=OTTHUMG00000000958.1 +chr1 HAVANA transcript 14404 29570 . - . ID=ENST00000488147.1;Parent=ENSG00000227232.5;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 29534 29570 . - . ID=exon:ENST00000488147.1:1;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=1;exon_id=ENSE00001890219.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 24738 24891 . - . ID=exon:ENST00000488147.1:2;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=2;exon_id=ENSE00003507205.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 18268 18366 . - . ID=exon:ENST00000488147.1:3;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=3;exon_id=ENSE00003477500.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 17915 18061 . - . ID=exon:ENST00000488147.1:4;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=4;exon_id=ENSE00003565697.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 17606 17742 . - . ID=exon:ENST00000488147.1:5;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=5;exon_id=ENSE00003475637.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 17233 17368 . - . ID=exon:ENST00000488147.1:6;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=6;exon_id=ENSE00003502542.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 16858 17055 . - . ID=exon:ENST00000488147.1:7;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=7;exon_id=ENSE00003553898.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 16607 16765 . - . ID=exon:ENST00000488147.1:8;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=8;exon_id=ENSE00003621279.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 15796 15947 . - . ID=exon:ENST00000488147.1:9;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=9;exon_id=ENSE00002030414.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 15005 15038 . - . ID=exon:ENST00000488147.1:10;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=10;exon_id=ENSE00001935574.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 HAVANA exon 14404 14501 . - . ID=exon:ENST00000488147.1:11;Parent=ENST00000488147.1;gene_id=ENSG00000227232.5;transcript_id=ENST00000488147.1;gene_type=unprocessed_pseudogene;gene_name=WASH7P;transcript_type=unprocessed_pseudogene;transcript_name=WASH7P-201;exon_number=11;exon_id=ENSE00001843071.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000000958.1;havana_transcript=OTTHUMT00000002839.1 +chr1 ENSEMBL gene 17369 17436 . - . ID=ENSG00000278267.1;gene_id=ENSG00000278267.1;gene_type=miRNA;gene_name=MIR6859-1;level=3 +chr1 ENSEMBL transcript 17369 17436 . - . ID=ENST00000619216.1;Parent=ENSG00000278267.1;gene_id=ENSG00000278267.1;transcript_id=ENST00000619216.1;gene_type=miRNA;gene_name=MIR6859-1;transcript_type=miRNA;transcript_name=MIR6859-1-201;level=3;transcript_support_level=NA;tag=basic +chr1 ENSEMBL exon 17369 17436 . - . ID=exon:ENST00000619216.1:1;Parent=ENST00000619216.1;gene_id=ENSG00000278267.1;transcript_id=ENST00000619216.1;gene_type=miRNA;gene_name=MIR6859-1;transcript_type=miRNA;transcript_name=MIR6859-1-201;exon_number=1;exon_id=ENSE00003746039.1;level=3;transcript_support_level=NA;tag=basic +chr1 HAVANA gene 29554 31109 . + . ID=ENSG00000243485.5;gene_id=ENSG00000243485.5;gene_type=lincRNA;gene_name=MIR1302-2HG;level=2;tag=ncRNA_host;havana_gene=OTTHUMG00000000959.2 +chr1 HAVANA transcript 29554 31097 . + . ID=ENST00000473358.1;Parent=ENSG00000243485.5;gene_id=ENSG00000243485.5;transcript_id=ENST00000473358.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-202;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,dotter_confirmed,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +chr1 HAVANA exon 29554 30039 . + . ID=exon:ENST00000473358.1:1;Parent=ENST00000473358.1;gene_id=ENSG00000243485.5;transcript_id=ENST00000473358.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-202;exon_number=1;exon_id=ENSE00001947070.1;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,dotter_confirmed,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +chr1 HAVANA exon 30564 30667 . + . ID=exon:ENST00000473358.1:2;Parent=ENST00000473358.1;gene_id=ENSG00000243485.5;transcript_id=ENST00000473358.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-202;exon_number=2;exon_id=ENSE00001922571.1;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,dotter_confirmed,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +chr1 HAVANA exon 30976 31097 . + . ID=exon:ENST00000473358.1:3;Parent=ENST00000473358.1;gene_id=ENSG00000243485.5;transcript_id=ENST00000473358.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-202;exon_number=3;exon_id=ENSE00001827679.1;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,dotter_confirmed,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002840.1 +chr1 HAVANA transcript 30267 31109 . + . ID=ENST00000469289.1;Parent=ENSG00000243485.5;gene_id=ENSG00000243485.5;transcript_id=ENST00000469289.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-201;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2 +chr1 HAVANA exon 30267 30667 . + . ID=exon:ENST00000469289.1:1;Parent=ENST00000469289.1;gene_id=ENSG00000243485.5;transcript_id=ENST00000469289.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-201;exon_number=1;exon_id=ENSE00001841699.1;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2 +chr1 HAVANA exon 30976 31109 . + . ID=exon:ENST00000469289.1:2;Parent=ENST00000469289.1;gene_id=ENSG00000243485.5;transcript_id=ENST00000469289.1;gene_type=lincRNA;gene_name=MIR1302-2HG;transcript_type=lincRNA;transcript_name=MIR1302-2HG-201;exon_number=2;exon_id=ENSE00001890064.1;level=2;transcript_support_level=5;tag=not_best_in_genome_evidence,basic;havana_gene=OTTHUMG00000000959.2;havana_transcript=OTTHUMT00000002841.2 +chr1 ENSEMBL gene 30366 30503 . + . ID=ENSG00000284332.1;gene_id=ENSG00000284332.1;gene_type=miRNA;gene_name=MIR1302-2;level=3 +chr1 ENSEMBL transcript 30366 30503 . + . ID=ENST00000607096.1;Parent=ENSG00000284332.1;gene_id=ENSG00000284332.1;transcript_id=ENST00000607096.1;gene_type=miRNA;gene_name=MIR1302-2;transcript_type=miRNA;transcript_name=MIR1302-2-201;level=3;transcript_support_level=NA;tag=basic +chr1 ENSEMBL exon 30366 30503 . + . ID=exon:ENST00000607096.1:1;Parent=ENST00000607096.1;gene_id=ENSG00000284332.1;transcript_id=ENST00000607096.1;gene_type=miRNA;gene_name=MIR1302-2;transcript_type=miRNA;transcript_name=MIR1302-2-201;exon_number=1;exon_id=ENSE00003695741.1;level=3;transcript_support_level=NA;tag=basic +chr1 HAVANA gene 34554 36081 . - . ID=ENSG00000237613.2;gene_id=ENSG00000237613.2;gene_type=lincRNA;gene_name=FAM138A;level=2;havana_gene=OTTHUMG00000000960.1 +chr1 HAVANA transcript 34554 36081 . - . ID=ENST00000417324.1;Parent=ENSG00000237613.2;gene_id=ENSG00000237613.2;transcript_id=ENST00000417324.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-201;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +chr1 HAVANA exon 35721 36081 . - . ID=exon:ENST00000417324.1:1;Parent=ENST00000417324.1;gene_id=ENSG00000237613.2;transcript_id=ENST00000417324.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-201;exon_number=1;exon_id=ENSE00001656588.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +chr1 HAVANA exon 35277 35481 . - . ID=exon:ENST00000417324.1:2;Parent=ENST00000417324.1;gene_id=ENSG00000237613.2;transcript_id=ENST00000417324.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-201;exon_number=2;exon_id=ENSE00001669267.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +chr1 HAVANA exon 34554 35174 . - . ID=exon:ENST00000417324.1:3;Parent=ENST00000417324.1;gene_id=ENSG00000237613.2;transcript_id=ENST00000417324.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-201;exon_number=3;exon_id=ENSE00001727627.1;level=2;transcript_support_level=1;tag=basic;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002842.1 +chr1 HAVANA transcript 35245 36073 . - . ID=ENST00000461467.1;Parent=ENSG00000237613.2;gene_id=ENSG00000237613.2;transcript_id=ENST00000461467.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-202;level=2;transcript_support_level=3;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1 +chr1 HAVANA exon 35721 36073 . - . ID=exon:ENST00000461467.1:1;Parent=ENST00000461467.1;gene_id=ENSG00000237613.2;transcript_id=ENST00000461467.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-202;exon_number=1;exon_id=ENSE00001618781.2;level=2;transcript_support_level=3;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1 +chr1 HAVANA exon 35245 35481 . - . ID=exon:ENST00000461467.1:2;Parent=ENST00000461467.1;gene_id=ENSG00000237613.2;transcript_id=ENST00000461467.1;gene_type=lincRNA;gene_name=FAM138A;transcript_type=lincRNA;transcript_name=FAM138A-202;exon_number=2;exon_id=ENSE00001874421.1;level=2;transcript_support_level=3;havana_gene=OTTHUMG00000000960.1;havana_transcript=OTTHUMT00000002843.1 +chr1 HAVANA gene 52473 53312 . + . ID=ENSG00000268020.3;gene_id=ENSG00000268020.3;gene_type=unprocessed_pseudogene;gene_name=OR4G4P;level=2;havana_gene=OTTHUMG00000185779.1 +chr1 HAVANA transcript 52473 53312 . + . ID=ENST00000606857.1;Parent=ENSG00000268020.3;gene_id=ENSG00000268020.3;transcript_id=ENST00000606857.1;gene_type=unprocessed_pseudogene;gene_name=OR4G4P;transcript_type=unprocessed_pseudogene;transcript_name=OR4G4P-201;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000185779.1;havana_transcript=OTTHUMT00000471235.1 +chr1 HAVANA exon 52473 53312 . + . ID=exon:ENST00000606857.1:1;Parent=ENST00000606857.1;gene_id=ENSG00000268020.3;transcript_id=ENST00000606857.1;gene_type=unprocessed_pseudogene;gene_name=OR4G4P;transcript_type=unprocessed_pseudogene;transcript_name=OR4G4P-201;exon_number=1;exon_id=ENSE00003698237.1;level=2;transcript_support_level=NA;ont=PGO:0000005;tag=basic;havana_gene=OTTHUMG00000185779.1;havana_transcript=OTTHUMT00000471235.1 +chr1 HAVANA gene 57598 64116 . + . ID=ENSG00000240361.2;gene_id=ENSG00000240361.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;level=2;havana_gene=OTTHUMG00000001095.3 +chr1 HAVANA transcript 57598 64116 . + . ID=ENST00000642116.1;Parent=ENSG00000240361.2;gene_id=ENSG00000240361.2;transcript_id=ENST00000642116.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=processed_transcript;transcript_name=OR4G11P-202;level=2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000492680.1 +chr1 HAVANA exon 57598 57653 . + . ID=exon:ENST00000642116.1:1;Parent=ENST00000642116.1;gene_id=ENSG00000240361.2;transcript_id=ENST00000642116.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=processed_transcript;transcript_name=OR4G11P-202;exon_number=1;exon_id=ENSE00003812686.1;level=2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000492680.1 +chr1 HAVANA exon 58700 58856 . + . ID=exon:ENST00000642116.1:2;Parent=ENST00000642116.1;gene_id=ENSG00000240361.2;transcript_id=ENST00000642116.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=processed_transcript;transcript_name=OR4G11P-202;exon_number=2;exon_id=ENSE00003812505.1;level=2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000492680.1 +chr1 HAVANA exon 62916 64116 . + . ID=exon:ENST00000642116.1:3;Parent=ENST00000642116.1;gene_id=ENSG00000240361.2;transcript_id=ENST00000642116.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=processed_transcript;transcript_name=OR4G11P-202;exon_number=3;exon_id=ENSE00003811818.1;level=2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000492680.1 +chr1 HAVANA transcript 62949 63887 . + . ID=ENST00000492842.2;Parent=ENSG00000240361.2;gene_id=ENSG00000240361.2;transcript_id=ENST00000492842.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=OR4G11P-201;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000003224.3 +chr1 HAVANA exon 62949 63887 . + . ID=exon:ENST00000492842.2:1;Parent=ENST00000492842.2;gene_id=ENSG00000240361.2;transcript_id=ENST00000492842.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=OR4G11P;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=OR4G11P-201;exon_number=1;exon_id=ENSE00001830178.2;level=2;transcript_support_level=NA;ont=PGO:0000005,PGO:0000019;tag=basic;havana_gene=OTTHUMG00000001095.3;havana_transcript=OTTHUMT00000003224.3 +chr1 HAVANA gene 65419 71585 . + . ID=ENSG00000186092.6;gene_id=ENSG00000186092.6;gene_type=protein_coding;gene_name=OR4F5;level=2;havana_gene=OTTHUMG00000001094.4 +chr1 HAVANA transcript 65419 71585 . + . ID=ENST00000641515.2;Parent=ENSG00000186092.6;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA exon 65419 65433 . + . ID=exon:ENST00000641515.2:1;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=1;exon_id=ENSE00003812156.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA exon 65520 65573 . + . ID=exon:ENST00000641515.2:2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=2;exon_id=ENSE00003813641.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA CDS 65565 65573 . + 0 ID=CDS:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=2;exon_id=ENSE00003813641.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA start_codon 65565 65567 . + 0 ID=start_codon:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=2;exon_id=ENSE00003813641.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA exon 69037 71585 . + . ID=exon:ENST00000641515.2:3;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=3;exon_id=ENSE00003813949.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA CDS 69037 70008 . + 0 ID=CDS:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=3;exon_id=ENSE00003813949.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA stop_codon 70006 70008 . + 0 ID=stop_codon:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=3;exon_id=ENSE00003813949.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA five_prime_UTR 65419 65433 . + . ID=UTR5:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=1;exon_id=ENSE00003812156.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA five_prime_UTR 65520 65564 . + . ID=UTR5:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=2;exon_id=ENSE00003813641.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 HAVANA three_prime_UTR 70009 71585 . + . ID=UTR3:ENST00000641515.2;Parent=ENST00000641515.2;gene_id=ENSG00000186092.6;transcript_id=ENST00000641515.2;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-202;exon_number=3;exon_id=ENSE00003813949.1;level=2;protein_id=ENSP00000493376.2;tag=RNA_Seq_supported_partial,basic;havana_gene=OTTHUMG00000001094.4;havana_transcript=OTTHUMT00000003223.4 +chr1 ENSEMBL transcript 69055 70108 . + . ID=ENST00000335137.4;Parent=ENSG00000186092.6;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL exon 69055 70108 . + . ID=exon:ENST00000335137.4:1;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL CDS 69091 70008 . + 0 ID=CDS:ENST00000335137.4;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL start_codon 69091 69093 . + 0 ID=start_codon:ENST00000335137.4;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL stop_codon 70006 70008 . + 0 ID=stop_codon:ENST00000335137.4;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL five_prime_UTR 69055 69090 . + . ID=UTR5:ENST00000335137.4;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 +chr1 ENSEMBL three_prime_UTR 70009 70108 . + . ID=UTR3:ENST00000335137.4;Parent=ENST00000335137.4;gene_id=ENSG00000186092.6;transcript_id=ENST00000335137.4;gene_type=protein_coding;gene_name=OR4F5;transcript_type=protein_coding;transcript_name=OR4F5-201;exon_number=1;exon_id=ENSE00002319515.2;level=3;protein_id=ENSP00000334393.3;transcript_support_level=NA;tag=basic,appris_principal_1,CCDS;ccdsid=CCDS30547.1;havana_gene=OTTHUMG00000001094.4 diff --git a/tests/test1/data/small.gencode.v29.gtf b/tests/test1/data/small.gencode.v29.gtf new file mode 100644 index 00000000..9407c482 --- /dev/null +++ b/tests/test1/data/small.gencode.v29.gtf @@ -0,0 +1,81 @@ +##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94) +##provider: GENCODE +##contact: gencode-help@ebi.ac.uk +##format: gtf +##date: 2018-08-30 +chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; +chr1 HAVANA transcript 11869 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 11869 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1"; +chr1 HAVANA transcript 12010 13670 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12010 12057 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12179 12227 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12613 12697 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 3; exon_id "ENSE00001758273.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 12975 13052 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 4; exon_id "ENSE00001799933.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 13221 13374 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 5; exon_id "ENSE00001746346.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA exon 13453 13670 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; exon_number 6; exon_id "ENSE00001863096.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; +chr1 HAVANA gene 14404 29570 . - . gene_id "ENSG00000227232.5"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; level 2; havana_gene "OTTHUMG00000000958.1"; +chr1 HAVANA transcript 14404 29570 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 29534 29570 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 1; exon_id "ENSE00001890219.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 24738 24891 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 2; exon_id "ENSE00003507205.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 18268 18366 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 3; exon_id "ENSE00003477500.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17915 18061 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 4; exon_id "ENSE00003565697.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17606 17742 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 5; exon_id "ENSE00003475637.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 17233 17368 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 6; exon_id "ENSE00003502542.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 16858 17055 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 7; exon_id "ENSE00003553898.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 16607 16765 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 8; exon_id "ENSE00003621279.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 15796 15947 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 9; exon_id "ENSE00002030414.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 15005 15038 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 10; exon_id "ENSE00001935574.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 HAVANA exon 14404 14501 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-201"; exon_number 11; exon_id "ENSE00001843071.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; +chr1 ENSEMBL gene 17369 17436 . - . gene_id "ENSG00000278267.1"; gene_type "miRNA"; gene_name "MIR6859-1"; level 3; +chr1 ENSEMBL transcript 17369 17436 . - . gene_id "ENSG00000278267.1"; transcript_id "ENST00000619216.1"; gene_type "miRNA"; gene_name "MIR6859-1"; transcript_type "miRNA"; transcript_name "MIR6859-1-201"; level 3; transcript_support_level "NA"; tag "basic"; +chr1 ENSEMBL exon 17369 17436 . - . gene_id "ENSG00000278267.1"; transcript_id "ENST00000619216.1"; gene_type "miRNA"; gene_name "MIR6859-1"; transcript_type "miRNA"; transcript_name "MIR6859-1-201"; exon_number 1; exon_id "ENSE00003746039.1"; level 3; transcript_support_level "NA"; tag "basic"; +chr1 HAVANA gene 29554 31109 . + . gene_id "ENSG00000243485.5"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; level 2; tag "ncRNA_host"; havana_gene "OTTHUMG00000000959.2"; +chr1 HAVANA transcript 29554 31097 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-202"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 29554 30039 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-202"; exon_number 1; exon_id "ENSE00001947070.1"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 30564 30667 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-202"; exon_number 2; exon_id "ENSE00001922571.1"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA exon 30976 31097 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000473358.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-202"; exon_number 3; exon_id "ENSE00001827679.1"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "dotter_confirmed"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002840.1"; +chr1 HAVANA transcript 30267 31109 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-201"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 HAVANA exon 30267 30667 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-201"; exon_number 1; exon_id "ENSE00001841699.1"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 HAVANA exon 30976 31109 . + . gene_id "ENSG00000243485.5"; transcript_id "ENST00000469289.1"; gene_type "lincRNA"; gene_name "MIR1302-2HG"; transcript_type "lincRNA"; transcript_name "MIR1302-2HG-201"; exon_number 2; exon_id "ENSE00001890064.1"; level 2; transcript_support_level "5"; tag "not_best_in_genome_evidence"; tag "basic"; havana_gene "OTTHUMG00000000959.2"; havana_transcript "OTTHUMT00000002841.2"; +chr1 ENSEMBL gene 30366 30503 . + . gene_id "ENSG00000284332.1"; gene_type "miRNA"; gene_name "MIR1302-2"; level 3; +chr1 ENSEMBL transcript 30366 30503 . + . gene_id "ENSG00000284332.1"; transcript_id "ENST00000607096.1"; gene_type "miRNA"; gene_name "MIR1302-2"; transcript_type "miRNA"; transcript_name "MIR1302-2-201"; level 3; transcript_support_level "NA"; tag "basic"; +chr1 ENSEMBL exon 30366 30503 . + . gene_id "ENSG00000284332.1"; transcript_id "ENST00000607096.1"; gene_type "miRNA"; gene_name "MIR1302-2"; transcript_type "miRNA"; transcript_name "MIR1302-2-201"; exon_number 1; exon_id "ENSE00003695741.1"; level 3; transcript_support_level "NA"; tag "basic"; +chr1 HAVANA gene 34554 36081 . - . gene_id "ENSG00000237613.2"; gene_type "lincRNA"; gene_name "FAM138A"; level 2; havana_gene "OTTHUMG00000000960.1"; +chr1 HAVANA transcript 34554 36081 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-201"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 35721 36081 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-201"; exon_number 1; exon_id "ENSE00001656588.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 35277 35481 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-201"; exon_number 2; exon_id "ENSE00001669267.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA exon 34554 35174 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000417324.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-201"; exon_number 3; exon_id "ENSE00001727627.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002842.1"; +chr1 HAVANA transcript 35245 36073 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-202"; level 2; transcript_support_level "3"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA exon 35721 36073 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-202"; exon_number 1; exon_id "ENSE00001618781.2"; level 2; transcript_support_level "3"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA exon 35245 35481 . - . gene_id "ENSG00000237613.2"; transcript_id "ENST00000461467.1"; gene_type "lincRNA"; gene_name "FAM138A"; transcript_type "lincRNA"; transcript_name "FAM138A-202"; exon_number 2; exon_id "ENSE00001874421.1"; level 2; transcript_support_level "3"; havana_gene "OTTHUMG00000000960.1"; havana_transcript "OTTHUMT00000002843.1"; +chr1 HAVANA gene 52473 53312 . + . gene_id "ENSG00000268020.3"; gene_type "unprocessed_pseudogene"; gene_name "OR4G4P"; level 2; havana_gene "OTTHUMG00000185779.1"; +chr1 HAVANA transcript 52473 53312 . + . gene_id "ENSG00000268020.3"; transcript_id "ENST00000606857.1"; gene_type "unprocessed_pseudogene"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_name "OR4G4P-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000185779.1"; havana_transcript "OTTHUMT00000471235.1"; +chr1 HAVANA exon 52473 53312 . + . gene_id "ENSG00000268020.3"; transcript_id "ENST00000606857.1"; gene_type "unprocessed_pseudogene"; gene_name "OR4G4P"; transcript_type "unprocessed_pseudogene"; transcript_name "OR4G4P-201"; exon_number 1; exon_id "ENSE00003698237.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000185779.1"; havana_transcript "OTTHUMT00000471235.1"; +chr1 HAVANA gene 57598 64116 . + . gene_id "ENSG00000240361.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; level 2; havana_gene "OTTHUMG00000001095.3"; +chr1 HAVANA transcript 57598 64116 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000642116.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "processed_transcript"; transcript_name "OR4G11P-202"; level 2; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000492680.1"; +chr1 HAVANA exon 57598 57653 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000642116.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "processed_transcript"; transcript_name "OR4G11P-202"; exon_number 1; exon_id "ENSE00003812686.1"; level 2; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000492680.1"; +chr1 HAVANA exon 58700 58856 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000642116.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "processed_transcript"; transcript_name "OR4G11P-202"; exon_number 2; exon_id "ENSE00003812505.1"; level 2; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000492680.1"; +chr1 HAVANA exon 62916 64116 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000642116.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "processed_transcript"; transcript_name "OR4G11P-202"; exon_number 3; exon_id "ENSE00003811818.1"; level 2; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000492680.1"; +chr1 HAVANA transcript 62949 63887 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000492842.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000003224.3"; +chr1 HAVANA exon 62949 63887 . + . gene_id "ENSG00000240361.2"; transcript_id "ENST00000492842.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "OR4G11P"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "OR4G11P-201"; exon_number 1; exon_id "ENSE00001830178.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000001095.3"; havana_transcript "OTTHUMT00000003224.3"; +chr1 HAVANA gene 65419 71585 . + . gene_id "ENSG00000186092.6"; gene_type "protein_coding"; gene_name "OR4F5"; level 2; havana_gene "OTTHUMG00000001094.4"; +chr1 HAVANA transcript 65419 71585 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA exon 65419 65433 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 1; exon_id "ENSE00003812156.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA exon 65520 65573 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA CDS 65565 65573 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA start_codon 65565 65567 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA exon 69037 71585 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA CDS 69037 70005 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA stop_codon 70006 70008 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA UTR 65419 65433 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 1; exon_id "ENSE00003812156.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA UTR 65520 65564 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 2; exon_id "ENSE00003813641.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 HAVANA UTR 70006 71585 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000641515.2"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-202"; exon_number 3; exon_id "ENSE00003813949.1"; level 2; protein_id "ENSP00000493376.2"; tag "RNA_Seq_supported_partial"; tag "basic"; havana_gene "OTTHUMG00000001094.4"; havana_transcript "OTTHUMT00000003223.4"; +chr1 ENSEMBL transcript 69055 70108 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL exon 69055 70108 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL CDS 69091 70005 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL start_codon 69091 69093 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL stop_codon 70006 70008 . + 0 gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL UTR 69055 69090 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; +chr1 ENSEMBL UTR 70006 70108 . + . gene_id "ENSG00000186092.6"; transcript_id "ENST00000335137.4"; gene_type "protein_coding"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_name "OR4F5-201"; exon_number 1; exon_id "ENSE00002319515.2"; level 3; protein_id "ENSP00000334393.3"; transcript_support_level "NA"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.4"; diff --git a/tests/test1/data/test1_1.fq b/tests/test1/data/test1_1.fq new file mode 100644 index 00000000..68843e93 --- /dev/null +++ b/tests/test1/data/test1_1.fq @@ -0,0 +1,24000 @@ +@test1_12000/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11998/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11996/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11994/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11992/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11990/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11988/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11986/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11984/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11982/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11980/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11978/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11976/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11974/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11972/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11970/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11968/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11966/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11964/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11962/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11960/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11958/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11956/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11954/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11952/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11950/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11948/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11946/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11944/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11942/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11940/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11938/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11936/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11934/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11932/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11930/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11928/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11926/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11924/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11922/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11920/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11918/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11916/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11914/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11912/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11910/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11908/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11906/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11904/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11902/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11900/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11898/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11896/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11894/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11892/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11890/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11888/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11886/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11884/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11882/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11880/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11878/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11876/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11874/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11872/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11870/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11868/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11866/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11864/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11862/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11860/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11858/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11856/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11854/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11852/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11850/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11848/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11846/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11844/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11842/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11840/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11838/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11836/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11834/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11832/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11830/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11828/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11826/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11824/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11822/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11820/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11818/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11816/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11814/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11812/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11810/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11808/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11806/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11804/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11802/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11800/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11798/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11796/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11794/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11792/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11790/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11788/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11786/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11784/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11782/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11780/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11778/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11776/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11774/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11772/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11770/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11768/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11766/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11764/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11762/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11760/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11758/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11756/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11754/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11752/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11750/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11748/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11746/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11744/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11742/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11740/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11738/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11736/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11734/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11732/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11730/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11728/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11726/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11724/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11722/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11720/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11718/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11716/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11714/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11712/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11710/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11708/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11706/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11704/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11702/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11700/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11698/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11696/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11694/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11692/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11690/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11688/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11686/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11684/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11682/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11680/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11678/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11676/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11674/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11672/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11670/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11668/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11666/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11664/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11662/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11660/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11658/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11656/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11654/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11652/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11650/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11648/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11646/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11644/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11642/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11640/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11638/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11636/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11634/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11632/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11630/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11628/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11626/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11624/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11622/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11620/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11618/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11616/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11614/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11612/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11610/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11608/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11606/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11604/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11602/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11600/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11598/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11596/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11594/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11592/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11590/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11588/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11586/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11584/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11582/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11580/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11578/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11576/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11574/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11572/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11570/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11568/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11566/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11564/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11562/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11560/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11558/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11556/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11554/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11552/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11550/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11548/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11546/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11544/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11542/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11540/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11538/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11536/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11534/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11532/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11530/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11528/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11526/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11524/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11522/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11520/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11518/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11516/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11514/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11512/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11510/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11508/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11506/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11504/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11502/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11500/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11498/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11496/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11494/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11492/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11490/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11488/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11486/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11484/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11482/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11480/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11478/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11476/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11474/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11472/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11470/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11468/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11466/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11464/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11462/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11460/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11458/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11456/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11454/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11452/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11450/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11448/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11446/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11444/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11442/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11440/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11438/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11436/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11434/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11432/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11430/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11428/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11426/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11424/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11422/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11420/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11418/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11416/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11414/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11412/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11410/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11408/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11406/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11404/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11402/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11400/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11398/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11396/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11394/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11392/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11390/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11388/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11386/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11384/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11382/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11380/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11378/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11376/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11374/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11372/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11370/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11368/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11366/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11364/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11362/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11360/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11358/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11356/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11354/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11352/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11350/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11348/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11346/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11344/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11342/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11340/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11338/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11336/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11334/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11332/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11330/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11328/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11326/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11324/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11322/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11320/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11318/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11316/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11314/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11312/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11310/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11308/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11306/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11304/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11302/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11300/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11298/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11296/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11294/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11292/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11290/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11288/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11286/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11284/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11282/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11280/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11278/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11276/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11274/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11272/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11270/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11268/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11266/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11264/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11262/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11260/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11258/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11256/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11254/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11252/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11250/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11248/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11246/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11244/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11242/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11240/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11238/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11236/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11234/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11232/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11230/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11228/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11226/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11224/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11222/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11220/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11218/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11216/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11214/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11212/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11210/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11208/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11206/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11204/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11202/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11200/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11198/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11196/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11194/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11192/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11190/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11188/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11186/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11184/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11182/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11180/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11178/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11176/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11174/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11172/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11170/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11168/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11166/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11164/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11162/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11160/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11158/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11156/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11154/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11152/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11150/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11148/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11146/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11144/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11142/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11140/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11138/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11136/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11134/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11132/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11130/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11128/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11126/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11124/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11122/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11120/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11118/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11116/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11114/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11112/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11110/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11108/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11106/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11104/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11102/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11100/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11098/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11096/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11094/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11092/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11090/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11088/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11086/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11084/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11082/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_11080/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11078/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11076/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11074/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11072/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11070/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11068/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11066/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11064/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11062/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11060/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11058/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11056/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11054/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11052/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11050/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_11048/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11046/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11044/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_11042/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_11040/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11038/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_11036/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11034/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11032/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11030/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11028/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11026/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_11024/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_11022/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11020/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11018/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11016/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_11014/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_11012/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_11010/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_11008/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_11006/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_11004/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_11002/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_11000/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10998/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10996/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10994/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10992/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10990/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10988/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10986/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10984/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10982/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10980/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10978/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10976/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10974/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10972/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10970/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10968/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10966/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10964/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10962/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10960/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10958/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10956/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10954/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10952/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10950/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10948/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10946/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10944/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10942/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10940/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10938/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10936/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10934/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10932/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10930/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10928/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10926/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10924/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10922/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10920/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10918/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10916/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10914/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10912/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10910/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10908/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10906/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10904/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10902/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10900/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10898/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10896/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10894/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10892/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10890/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10888/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10886/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10884/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10882/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10880/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10878/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10876/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10874/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10872/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10870/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10868/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10866/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10864/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10862/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10860/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10858/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10856/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10854/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10852/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10850/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10848/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10846/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10844/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10842/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10840/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10838/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10836/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10834/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10832/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10830/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10828/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10826/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10824/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10822/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10820/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10818/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10816/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10814/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10812/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10810/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10808/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10806/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10804/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10802/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10800/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10798/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10796/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10794/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10792/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10790/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10788/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10786/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10784/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10782/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10780/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10778/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10776/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10774/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10772/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10770/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10768/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10766/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10764/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10762/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10760/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10758/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10756/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10754/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10752/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10750/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10748/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10746/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10744/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10742/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10740/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10738/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10736/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10734/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10732/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10730/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10728/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10726/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10724/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10722/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10720/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10718/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10716/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10714/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10712/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10710/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10708/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10706/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10704/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10702/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10700/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10698/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10696/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10694/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10692/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10690/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10688/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10686/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10684/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10682/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10680/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10678/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10676/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10674/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10672/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10670/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10668/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10666/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10664/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10662/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10660/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10658/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10656/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10654/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10652/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10650/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10648/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10646/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10644/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10642/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10640/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10638/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10636/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10634/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10632/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10630/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10628/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10626/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10624/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10622/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10620/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10618/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10616/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10614/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10612/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10610/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10608/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10606/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10604/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10602/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10600/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10598/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10596/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10594/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10592/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10590/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10588/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10586/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10584/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10582/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10580/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10578/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10576/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10574/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10572/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10570/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10568/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10566/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10564/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10562/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10560/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10558/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10556/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10554/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10552/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10550/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10548/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10546/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10544/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10542/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10540/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10538/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10536/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10534/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10532/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10530/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10528/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10526/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10524/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10522/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10520/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10518/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10516/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10514/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10512/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10510/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10508/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10506/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10504/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10502/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10500/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10498/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10496/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10494/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10492/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10490/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10488/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10486/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10484/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10482/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10480/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10478/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10476/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10474/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10472/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10470/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10468/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10466/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10464/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10462/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10460/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10458/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10456/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10454/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10452/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10450/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10448/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10446/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10444/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10442/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10440/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10438/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10436/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10434/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10432/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10430/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10428/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10426/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10424/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10422/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10420/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10418/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10416/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10414/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10412/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10410/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10408/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10406/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10404/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10402/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10400/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10398/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10396/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10394/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10392/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10390/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10388/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10386/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10384/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10382/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10380/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10378/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10376/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10374/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10372/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10370/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10368/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10366/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10364/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10362/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10360/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10358/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10356/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10354/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10352/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10350/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10348/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10346/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10344/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10342/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10340/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10338/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10336/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10334/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10332/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10330/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10328/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10326/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10324/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10322/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10320/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10318/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10316/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10314/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10312/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10310/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10308/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10306/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10304/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10302/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10300/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10298/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10296/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10294/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10292/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10290/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10288/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10286/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10284/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10282/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10280/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10278/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10276/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10274/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10272/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10270/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10268/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10266/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10264/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10262/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10260/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10258/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10256/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10254/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10252/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10250/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10248/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10246/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10244/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10242/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10240/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10238/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10236/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10234/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10232/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10230/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10228/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10226/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10224/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10222/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10220/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10218/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10216/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10214/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10212/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10210/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10208/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10206/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10204/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10202/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10200/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10198/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10196/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10194/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10192/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10190/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10188/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10186/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10184/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10182/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10180/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10178/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10176/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10174/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10172/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10170/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10168/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10166/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10164/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10162/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10160/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10158/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10156/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10154/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10152/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10150/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10148/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10146/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10144/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10142/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10140/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10138/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10136/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10134/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10132/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10130/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10128/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10126/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10124/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10122/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10120/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10118/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10116/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10114/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10112/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10110/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10108/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10106/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10104/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10102/1 +GTACGTATATCGACG ++ +GGGGGGGGGGGGGGG +@test1_10100/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10098/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10096/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10094/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10092/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10090/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10088/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10086/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10084/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10082/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10080/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10078/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10076/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10074/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10072/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10070/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10068/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10066/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10064/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_10062/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10060/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10058/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10056/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10054/1 +ATCGACGTTCTGGTG ++ +GGGGGGGGGGGGGGG +@test1_10052/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10050/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10048/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10046/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10044/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10042/1 +TACGTATATCGACGT ++ +GGGGGGGGGGGGGGG +@test1_10040/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10038/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10036/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10034/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10032/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10030/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10028/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10026/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10024/1 +ATATCGACGTTCTGG ++ +GGGGGGGGGGGGGGG +@test1_10022/1 +AGGTACGTATATCGA ++ +GGGGGGGGGGGGGGG +@test1_10020/1 +CAGGTACGTATATCG ++ +GGGGGGGGGGGGGGG +@test1_10018/1 +TATCGACGTTCTGGT ++ +GGGGGGGGGGGGGGG +@test1_10016/1 +ACGTATATCGACGTT ++ +GGGGGGGGGGGGGGG +@test1_10014/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10012/1 +GTATATCGACGTTCT ++ +GGGGGGGGGGGGGGG +@test1_10010/1 +CGTATATCGACGTTC ++ +GGGGGGGGGGGGGGG +@test1_10008/1 +TATATCGACGTTCTG ++ +GGGGGGGGGGGGGGG +@test1_10006/1 +GGTACGTATATCGAC ++ +GGGGGGGGGGGGGGG +@test1_10004/1 +TCAGGTACGTATATC ++ +GGGGGGGGGGGGGGG +@test1_10002/1 +TTCAGGTACGTATAT ++ +GGGGGGGGGGGGGGG +@test1_10000/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9998/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9996/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9994/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9992/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9990/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9988/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9986/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9984/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9982/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9980/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9978/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9976/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9974/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9972/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9970/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9968/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9966/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9964/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9962/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9960/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9958/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9956/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9954/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9952/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9950/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9948/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9946/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9944/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9942/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9940/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9938/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9936/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9934/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9932/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9930/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9928/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9926/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9924/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9922/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9920/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9918/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9916/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9914/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9912/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9910/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9908/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9906/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9904/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9902/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9900/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9898/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9896/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9894/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9892/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9890/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9888/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9886/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9884/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9882/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9880/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9878/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9876/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9874/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9872/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9870/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9868/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG 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+@test1_9600/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9598/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9596/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9594/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9592/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9590/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9588/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9586/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9584/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9582/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9580/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9578/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9576/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9574/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9572/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9570/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9568/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9566/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9564/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9562/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9560/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9558/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9556/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9554/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9552/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9550/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9548/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9546/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9544/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9542/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9540/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9538/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9536/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9534/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9532/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9530/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9528/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9526/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9524/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9522/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9520/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9518/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9516/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9514/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9512/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9510/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9508/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9506/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9504/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9502/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9500/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9498/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9496/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9494/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9492/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9490/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9488/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9486/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9484/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9482/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9480/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9478/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9476/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9474/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9472/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9470/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_9468/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9466/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9464/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_9462/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9460/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_9458/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_9456/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_9454/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9452/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_9450/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG 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+@test1_8612/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8610/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8608/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8606/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8604/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8602/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_8600/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8598/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8596/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8594/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8592/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8590/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8588/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8586/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8584/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8582/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_8580/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8578/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8576/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG 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+@test1_8536/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8534/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8532/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8530/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8528/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_8526/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8524/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8522/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8520/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_8518/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8516/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8514/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_8512/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8510/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8508/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8506/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8504/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8502/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8500/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8498/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8496/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8494/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8492/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8490/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8488/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8486/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8484/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8482/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8480/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_8478/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8476/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8474/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_8472/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_8470/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8468/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8466/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_8464/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_8462/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG 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+@test1_7548/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7546/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7544/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7542/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7540/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_7538/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7536/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7534/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7532/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_7530/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7528/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7526/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_7524/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_7522/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_7520/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7518/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7516/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7514/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7512/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_7510/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_7508/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_7506/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_7504/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_7502/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_7500/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7498/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7496/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7494/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7492/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7490/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7488/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7486/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_7484/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_7482/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7480/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_7478/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_7476/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_7474/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG 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+@test1_2076/1 +ATGGTGATGGGTTGC ++ +GGGGGGGGGGGGGGG +@test1_2074/1 +GGTGATGGGTTGCGG ++ +GGGGGGGGGGGGGGG +@test1_2072/1 +GACGCACGCATGGTG ++ +GGGGGGGGGGGGGGG +@test1_2070/1 +TGATGGGTTGCGGAT ++ +GGGGGGGGGGGGGGG +@test1_2068/1 +GATGACGCACGCATG ++ +GGGGGGGGGGGGGGG +@test1_2066/1 +GGGTTGCGGATTCAG ++ +GGGGGGGGGGGGGGG +@test1_2064/1 +GCATGGTGATGGGTT ++ +GGGGGGGGGGGGGGG +@test1_2062/1 +TGACGCACGCATGGT ++ +GGGGGGGGGGGGGGG +@test1_2060/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_2058/1 +TTGCGGATTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_2056/1 +TGCGGATTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_2054/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_2052/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_2050/1 +CACGCATGGTGATGG ++ +GGGGGGGGGGGGGGG +@test1_2048/1 +GCATGGTGATGGGTT ++ +GGGGGGGGGGGGGGG +@test1_2046/1 +GTTGCGGATTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_2044/1 +TTGCGGATTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_2042/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_2040/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_2038/1 +CACGCATGGTGATGG ++ +GGGGGGGGGGGGGGG +@test1_2036/1 +CGCATGGTGATGGGT ++ +GGGGGGGGGGGGGGG +@test1_2034/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_2032/1 +CACGCATGGTGATGG ++ +GGGGGGGGGGGGGGG +@test1_2030/1 +CATGGTGATGGGTTG ++ +GGGGGGGGGGGGGGG +@test1_2028/1 +CGCACGCATGGTGAT ++ +GGGGGGGGGGGGGGG +@test1_2026/1 +GCACGCATGGTGATG ++ +GGGGGGGGGGGGGGG +@test1_2024/1 +TTGCGGATTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_2022/1 +ATGACGCACGCATGG ++ +GGGGGGGGGGGGGGG +@test1_2020/1 +GTTGCGGATTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_2018/1 +GGTTGCGGATTCAGG ++ +GGGGGGGGGGGGGGG +@test1_2016/1 +GCATGGTGATGGGTT ++ +GGGGGGGGGGGGGGG +@test1_2014/1 +GGTTGCGGATTCAGG ++ +GGGGGGGGGGGGGGG +@test1_2012/1 +CGGATTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_2010/1 +GATGACGCACGCATG ++ +GGGGGGGGGGGGGGG +@test1_2008/1 +CGCATGGTGATGGGT ++ +GGGGGGGGGGGGGGG +@test1_2006/1 +ACGCACGCATGGTGA ++ +GGGGGGGGGGGGGGG +@test1_2004/1 +GTTGCGGATTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_2002/1 +TGCGGATTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_2000/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1998/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1996/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1994/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1992/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1990/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1988/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1986/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1984/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1982/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1980/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1978/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1976/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1974/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1972/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1970/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1968/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1966/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1964/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1962/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1960/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1958/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1956/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1954/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1952/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1950/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1948/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1946/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1944/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1942/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1940/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1938/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1936/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1934/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1932/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1930/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1928/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1926/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1924/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1922/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1920/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1918/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1916/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1914/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1912/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1910/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1908/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1906/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1904/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1902/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1900/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1898/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1896/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1894/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1892/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1890/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1888/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG 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+@test1_1810/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1808/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1806/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1804/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1802/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1800/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1798/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1796/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1794/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1792/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1790/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1788/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1786/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1784/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1782/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1780/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1778/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1776/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1774/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1772/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1770/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1768/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1766/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1764/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1762/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1760/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1758/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1756/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1754/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1752/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1750/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1748/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1746/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1744/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1742/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1740/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1738/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1736/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1734/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1732/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1730/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1728/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1726/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1724/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1722/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1720/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1718/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1716/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1714/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1712/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1710/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1708/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1706/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1704/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1702/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1700/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1698/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1696/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1694/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1692/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1690/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1688/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1686/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1684/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1682/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1680/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1678/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1676/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1674/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1672/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1670/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1668/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1666/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1664/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1662/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1660/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1658/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1656/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1654/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1652/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1650/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1648/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1646/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1644/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1642/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1640/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1638/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1636/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1634/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1632/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1630/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1628/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1626/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1624/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1622/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1620/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1618/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1616/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1614/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1612/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1610/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1608/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1606/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1604/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1602/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_1600/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1598/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1596/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1594/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1592/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1590/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1588/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1586/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1584/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1582/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1580/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1578/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_1576/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1574/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1572/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1570/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1568/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1566/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1564/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1562/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1560/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1558/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1556/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_1554/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1552/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_1550/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1548/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1546/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG 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+@test1_1050/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1048/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1046/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1044/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1042/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1040/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1038/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1036/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1034/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1032/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1030/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_1028/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_1026/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_1024/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_1022/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_1020/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1018/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1016/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_1014/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_1012/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_1010/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_1008/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1006/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_1004/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_1002/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_1000/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_998/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_996/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_994/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_992/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_990/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_988/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_986/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_984/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_982/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_980/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_978/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_976/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_974/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_972/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_970/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_968/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_966/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_964/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_962/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_960/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_958/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_956/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_954/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_952/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_950/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_948/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_946/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_944/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_942/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_940/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_938/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_936/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_934/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_932/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_930/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_928/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_926/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_924/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_922/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_920/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_918/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_916/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_914/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_912/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_910/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_908/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_906/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_904/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_902/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_900/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_898/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_896/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_894/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_892/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_890/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_888/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_886/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_884/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_882/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_880/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_878/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_876/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_874/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_872/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_870/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_868/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_866/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_864/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_862/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_860/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_858/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_856/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_854/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_852/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_850/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_848/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_846/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_844/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_842/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_840/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_838/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_836/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_834/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_832/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_830/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_828/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_826/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_824/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_822/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_820/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_818/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_816/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_814/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_812/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_810/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_808/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_806/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_804/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_802/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_800/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_798/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_796/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_794/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_792/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_790/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_788/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_786/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_784/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_782/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_780/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_778/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_776/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_774/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_772/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_770/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_768/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_766/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_764/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_762/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_760/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_758/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_756/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_754/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_752/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_750/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_748/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_746/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_744/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_742/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_740/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_738/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_736/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_734/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_732/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_730/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_728/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_726/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_724/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_722/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_720/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_718/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_716/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_714/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_712/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_710/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_708/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_706/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_704/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_702/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_700/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_698/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_696/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_694/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_692/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_690/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_688/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_686/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_684/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_682/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_680/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_678/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_676/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_674/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_672/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_670/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_668/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_666/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_664/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_662/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_660/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_658/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_656/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_654/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_652/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_650/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_648/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_646/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_644/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_642/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_640/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_638/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_636/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_634/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_632/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_630/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_628/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_626/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_624/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_622/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_620/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_618/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_616/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_614/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_612/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_610/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_608/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_606/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_604/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_602/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_600/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_598/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_596/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_594/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_592/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_590/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_588/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_586/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_584/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_582/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_580/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_578/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_576/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_574/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_572/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_570/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_568/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_566/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_564/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_562/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_560/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_558/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_556/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_554/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_552/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_550/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_548/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_546/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_544/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_542/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_540/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_538/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_536/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_534/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_532/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_530/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_528/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_526/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_524/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_522/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_520/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_518/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_516/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_514/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_512/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_510/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_508/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_506/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_504/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_502/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_500/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_498/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_496/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_494/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_492/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_490/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_488/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_486/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_484/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_482/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_480/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_478/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_476/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_474/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_472/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_470/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_468/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_466/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_464/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_462/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_460/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_458/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_456/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_454/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_452/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_450/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_448/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_446/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_444/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_442/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_440/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_438/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_436/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_434/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_432/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_430/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_428/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_426/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_424/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_422/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_420/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_418/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_416/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_414/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_412/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_410/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_408/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_406/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_404/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_402/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_400/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_398/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_396/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_394/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_392/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_390/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_388/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_386/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_384/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_382/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_380/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_378/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_376/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_374/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_372/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_370/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_368/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_366/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_364/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_362/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_360/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_358/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_356/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_354/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_352/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_350/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_348/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_346/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_344/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_342/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_340/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_338/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_336/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_334/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_332/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_330/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_328/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_326/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_324/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_322/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_320/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_318/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_316/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_314/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_312/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_310/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_308/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_306/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_304/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_302/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_300/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_298/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_296/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_294/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_292/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_290/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_288/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_286/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_284/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_282/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_280/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_278/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_276/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_274/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_272/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_270/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_268/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_266/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_264/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_262/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_260/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_258/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_256/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_254/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_252/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_250/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_248/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_246/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_244/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_242/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_240/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_238/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_236/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_234/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_232/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_230/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_228/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_226/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_224/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_222/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_220/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_218/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_216/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_214/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_212/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_210/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_208/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_206/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_204/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_202/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_200/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_198/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_196/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_194/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_192/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_190/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_188/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_186/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_184/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_182/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_180/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_178/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_176/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_174/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_172/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_170/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_168/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_166/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_164/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_162/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_160/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_158/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_156/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_154/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_152/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_150/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_148/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_146/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_144/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_142/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_140/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_138/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_136/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_134/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_132/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_130/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_128/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_126/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_124/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_122/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_120/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_118/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_116/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_114/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_112/1 +TCGAGTTCAGGTACG ++ +GGGGGGGGGGGGGGG +@test1_110/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_108/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_106/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_104/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_102/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_100/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_98/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_96/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_94/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_92/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_90/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_88/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_86/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_84/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_82/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_80/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_78/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_76/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_74/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_72/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_70/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_68/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_66/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_64/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_62/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_60/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_58/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_56/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_54/1 +CAGGTACGTATAGTT ++ +GGGGGGGGGGGGGGG +@test1_52/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_50/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_48/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_46/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_44/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_42/1 +TACGTATAGTTGCTA ++ +GGGGGGGGGGGGGGG +@test1_40/1 +CGAGTTCAGGTACGT ++ +GGGGGGGGGGGGGGG +@test1_38/1 +TTCGAGTTCAGGTAC ++ +GGGGGGGGGGGGGGG +@test1_36/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_34/1 +AGTTCAGGTACGTAT ++ +GGGGGGGGGGGGGGG +@test1_32/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_30/1 +GTACGTATAGTTGCT ++ +GGGGGGGGGGGGGGG +@test1_28/1 +GTTCAGGTACGTATA ++ +GGGGGGGGGGGGGGG +@test1_26/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_24/1 +GTTCGAGTTCAGGTA ++ +GGGGGGGGGGGGGGG +@test1_22/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_20/1 +AGTTCGAGTTCAGGT ++ +GGGGGGGGGGGGGGG +@test1_18/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_16/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG +@test1_14/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_12/1 +TCAGGTACGTATAGT ++ +GGGGGGGGGGGGGGG +@test1_10/1 +ACGTATAGTTGCTAA ++ +GGGGGGGGGGGGGGG +@test1_8/1 +TTCAGGTACGTATAG ++ +GGGGGGGGGGGGGGG +@test1_6/1 +GGTACGTATAGTTGC ++ +GGGGGGGGGGGGGGG +@test1_4/1 +AGGTACGTATAGTTG ++ +GGGGGGGGGGGGGGG +@test1_2/1 +GAGTTCAGGTACGTA ++ +GGGGGGGGGGGGGGG diff --git a/tests/test1/data/test1neg.fa b/tests/test1/data/test1neg.fa new file mode 100644 index 00000000..d4642908 --- /dev/null +++ b/tests/test1/data/test1neg.fa @@ -0,0 +1,2 @@ +>X dna:chromosome chromosome:GRCh37:1:1:155270560:1 +ATGTATATCAACATGGCTGCCTTACCCAATTGGGTAACAAAAGGTCTACCACCAGAACGTCGACTACTTAGCAACTATACGTACCTGAACTCGAACTTACTCCGCAACCCATCTCCAATACCACCATGCGTGCGTCATCTTACACATTAC \ No newline at end of file diff --git a/tests/test1/data/test1neg.gtf b/tests/test1/data/test1neg.gtf new file mode 100644 index 00000000..9d93bc54 --- /dev/null +++ b/tests/test1/data/test1neg.gtf @@ -0,0 +1,50 @@ +X HAVANA gene 1 150 . - . gene_id "GENE1"; transcript_id "GENE1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD"; level 2; havana_gene "OTTHUMG00000022001.1"; +X HAVANA transcript 61 146 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 122 146 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 122 139 . - 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 137 139 . - 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 101 112 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 101 112 . - 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 61 89 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 78 89 . - 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 75 77 . - 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 140 146 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 61 77 . - . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 41 101 . - . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 76 101 . - . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 76 90 . - 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 88 90 . - 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 49 63 . - . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 49 63 . - 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 46 48 . - 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 91 101 . - . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 41 48 . - . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 101 146 . - . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 122 146 . - . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 122 139 . - 1 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 136 138 . - 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 101 112 . - . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 109 112 . - 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 106 108 . - 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 140 146 . - . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 101 108 . - . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 41 146 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 125 146 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 125 136 . - 2 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 132 134 . - 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 101 112 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 101 112 . - 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 76 84 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 76 84 . - 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 49 63 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 49 63 . - 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 46 48 . - 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 137 146 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 41 48 . - . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 63 101 . - . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 67 97 . - . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 67 97 . - 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 95 97 . - 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 64 66 . - 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 98 101 . - . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 63 66 . - . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; diff --git a/tests/test1/data/test1neg.maf b/tests/test1/data/test1neg.maf new file mode 100644 index 00000000..cf541a0a --- /dev/null +++ b/tests/test1/data/test1neg.maf @@ -0,0 +1,2 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER COSMIC CENTERS CONTEXT DBVS NCALLERS +JAKMIP3 0 . GRCh37 X 112 112 - Silent SNP T T C rs763531628 . test1neg test1neg C C . . . . . . . . . . . . . . . c.2169C>T p.%3D p.D723D ENST00000298622 18/24 82 16 65 123 123 0 JAKMIP3,synonymous_variant,p.%3D,ENST00000298622,;JAKMIP3,non_coding_transcript_exon_variant,,ENST00000477275,; T ENSG00000188385 ENST00000298622 Transcript synonymous_variant 2307 2169 723 D gaC/gaT rs763531628,COSM2148890 . . 1 JAKMIP3 HGNC 23523 protein_coding YES CCDS44494.1 ENSP00000298622 JKIP3_HUMAN . UPI000157482F . . . 18/24 . hmmpanther:PTHR18935:SF5,hmmpanther:PTHR18935 . . . . . . . . . . 0,1 . . . . . LOW . SNV . . 0,1 . . . . . . . . . . PASS NONE MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS CTGGACGAGGA byFrequency 5 diff --git a/tests/data/chrx.vcf b/tests/test1/data/test1neg.vcf similarity index 83% rename from tests/data/chrx.vcf rename to tests/test1/data/test1neg.vcf index b2a19a8a..afc72daa 100644 --- a/tests/data/chrx.vcf +++ b/tests/test1/data/test1neg.vcf @@ -27,6 +27,6 @@ ##INFO= ##reference=GRCh37 ##reference=GRCh37 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT OMM475.T -X 99889013 rs149201999 C A 100 PASS LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06 GT:DS:GL 0|0:0.050:-0.03,-1.17,-5.00 -X 99887500 rs146752890 C G 100 PASS AC=184;RSQ=0.8228;AVGPOST=0.9640;AN=2184;ERATE=0.0031;VT=SNP;AA=.;THETA=0.0127;LDAF=0.0902;SNPSOURCE=LOWCOV;AF=0.08;ASN_AF=0.08;AMR_AF=0.14;AFR_AF=0.08;EUR_AF=0.07 GT:DS:GL 0|1:1.000:-2.05,-0.01,-1.71 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test1neg +X 136 rs149201999 C G 100 PASS LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06 GT:DS:GL 1|1:0.050:-0.03,-1.17,-5.00 +X 130 rs149201999 C G 100 PASS LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06 GT:DS:GL 0|0:0.050:-0.03,-1.17,-5.00 diff --git a/tests/test1/data/test1pos.fa b/tests/test1/data/test1pos.fa new file mode 100644 index 00000000..94bd0fc8 --- /dev/null +++ b/tests/test1/data/test1pos.fa @@ -0,0 +1,2 @@ +>X dna:chromosome chromosome:GRCh37:X:1:155270560:1 +GTAATGTGTAAGATGACGCACGCATGGTGGTATTGGAGATGGGTTGCGGAGTAAGTTCGAGTTCAGGTACGTATAGTTGCTAAGTAGTCGACGTTCTGGTGGTAGACCTTTTGTTACCCAATTGGGTAAGGCAGCCATGTTGATATACAT \ No newline at end of file diff --git a/tests/test1/data/test1pos.gtf b/tests/test1/data/test1pos.gtf new file mode 100644 index 00000000..058ef258 --- /dev/null +++ b/tests/test1/data/test1pos.gtf @@ -0,0 +1,50 @@ +X HAVANA gene 1 150 . + . gene_id "GENE1"; transcript_id "GENE1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD"; level 2; havana_gene "OTTHUMG00000022001.1"; +X HAVANA transcript 5 90 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 5 29 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 12 29 . + 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 12 14 . + 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 39 50 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 39 50 . + 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 62 90 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 62 73 . + 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 74 76 . + 0 gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 5 11 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 74 90 . + . gene_id "GENE1"; transcript_id "TRANS1.1"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 50 110 . + . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 50 75 . + . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 61 75 . + 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 61 63 . + 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 88 102 . + . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 88 102 . + 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 103 105 . + 0 gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 50 60 . + . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 103 110 . + . gene_id "GENE1"; transcript_id "TRANS1.2"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 5 50 . + . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 5 29 . + . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 12 29 . + 1 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 13 15 . + 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 39 50 . + . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 39 42 . + 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 43 45 . + 0 gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 5 11 . + . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 43 50 . + . gene_id "GENE1"; transcript_id "TRANS1.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 5 110 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 5 26 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 15 26 . + 2 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 17 19 . + 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 39 50 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 39 50 . + 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 67 75 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 67 75 . + 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA exon 88 102 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA CDS 88 102 . + 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 103 105 . + 0 gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; exon_number 3; exon_id "exon1.3"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 5 14 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 103 110 . + . gene_id "GENE1"; transcript_id "TRANS1.4"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA transcript 50 88 . + . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA exon 54 84 . + . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057482.1"; +X HAVANA CDS 54 84 . + 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA start_codon 54 56 . + 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 1; exon_id "exon1.1"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA stop_codon 85 87 . + 0 gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; exon_number 2; exon_id "exon1.2"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 50 53 . + . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; +X HAVANA UTR 85 88 . + . gene_id "GENE1"; transcript_id "TRANS1.5"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "TNMD"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "TNMD-002"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS14469.1"; havana_gene "OTTHUMG00000022001.1"; havana_transcript "OTTHUMT00000057481.1"; diff --git a/tests/test1/data/test1pos.maf b/tests/test1/data/test1pos.maf new file mode 100644 index 00000000..8039c8fd --- /dev/null +++ b/tests/test1/data/test1pos.maf @@ -0,0 +1,2 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count all_effects Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER COSMIC CENTERS CONTEXT DBVS NCALLERS +JAKMIP3 0 . GRCh37 X 39 39 + Silent SNP A A G rs763531628 . test1pos test1pos C C . . . . . . . . . . . . . . . c.2169C>T p.%3D p.D723D ENST00000298622 18/24 82 16 65 123 123 0 JAKMIP3,synonymous_variant,p.%3D,ENST00000298622,;JAKMIP3,non_coding_transcript_exon_variant,,ENST00000477275,; T ENSG00000188385 ENST00000298622 Transcript synonymous_variant 2307 2169 723 D gaC/gaT rs763531628,COSM2148890 . . 1 JAKMIP3 HGNC 23523 protein_coding YES CCDS44494.1 ENSP00000298622 JKIP3_HUMAN . UPI000157482F . . . 18/24 . hmmpanther:PTHR18935:SF5,hmmpanther:PTHR18935 . . . . . . . . . . 0,1 . . . . . LOW . SNV . . 0,1 . . . . . . . . . . PASS NONE MUTECT|RADIA|SOMATICSNIPER|MUSE|VARSCANS CTGGACGAGGA byFrequency 5 diff --git a/tests/test1/data/test1pos.vcf b/tests/test1/data/test1pos.vcf new file mode 100644 index 00000000..cebcf87c --- /dev/null +++ b/tests/test1/data/test1pos.vcf @@ -0,0 +1,32 @@ +##fileformat=VCFv4.1 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##ALT= +##FORMAT= +##FORMAT= +##FORMAT= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##reference=GRCh37 +##reference=GRCh37 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test1pos +X 15 rs149201999 G C 100 PASS LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06 GT:DS:GL 1|1:0.050:-0.03,-1.17,-5.00 +X 21 rs149201999 G C 100 PASS LDAF=0.0649;RSQ=0.8652;AN=2184;ERATE=0.0046;VT=SNP;AA=.;AVGPOST=0.9799;THETA=0.0149;SNPSOURCE=LOWCOV;AC=134;AF=0.06;ASN_AF=0.04;AMR_AF=0.05;AFR_AF=0.10;EUR_AF=0.06 GT:DS:GL 0|0:0.050:-0.03,-1.17,-5.00 diff --git a/tests/test1/data/test1vcf.h5 b/tests/test1/data/test1vcf.h5 new file mode 100644 index 00000000..c67ee3ac Binary files /dev/null and b/tests/test1/data/test1vcf.h5 differ diff --git a/tests/test1/test1neg/germline_metadata.tsv.gz b/tests/test1/test1neg/germline_metadata.tsv.gz new file mode 100644 index 00000000..f170352d Binary files /dev/null and b/tests/test1/test1neg/germline_metadata.tsv.gz differ diff --git a/tests/test1/test1neg/germline_metadata_gt.tsv b/tests/test1/test1neg/germline_metadata_gt.tsv new file mode 100644 index 00000000..fc5b051d --- /dev/null +++ b/tests/test1/test1neg/germline_metadata_gt.tsv @@ -0,0 +1,5 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 2 GENE1 X - germline 0.333 1 . 1 . 1 . . 124;138;102;112 7,5 . 1338 +0.1 0 GENE1 X - germline 0.333 0 1 0 . 0 . . 124;139;100;112 7,5 0.0 1330 +0.2 2 GENE1 X - germline 0.333 1 . 1 . 1 . . 121;138;102;112 6,5 . 1470 +0.3 0 GENE1 X - germline 0.333 1 1 0 . 0 . . 121;139;100;112 6,5 1195.0 1450 diff --git a/tests/test1/test1neg/germline_peptides_gt.fa b/tests/test1/test1neg/germline_peptides_gt.fa new file mode 100644 index 00000000..8dcb3cb0 --- /dev/null +++ b/tests/test1/test1neg/germline_peptides_gt.fa @@ -0,0 +1,8 @@ +>0.0 GENE1 +ITHA +>0.1 GENE1 +DHARMMGCG +>0.2 GENE1 +ITHAW +>0.3 GENE1 +DHARMVMGCG diff --git a/tests/test1/test1neg/ref_metadata.tsv.gz b/tests/test1/test1neg/ref_metadata.tsv.gz new file mode 100644 index 00000000..42995b8d Binary files /dev/null and b/tests/test1/test1neg/ref_metadata.tsv.gz differ diff --git a/tests/test1/test1neg/ref_metadata_gt.tsv b/tests/test1/test1neg/ref_metadata_gt.tsv new file mode 100644 index 00000000..9b624560 --- /dev/null +++ b/tests/test1/test1neg/ref_metadata_gt.tsv @@ -0,0 +1,15 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 1 GENE1 X - ref 0.333 1 1 0 . 0 . . 124;134;101;112 7,5 0.0 1351 +0.1 2 GENE1 X - ref 0.333 1 . 1 . 1 . . 124;138;102;112 7,5 . 1338 +0.2 0 GENE1 X - ref 0.333 0 1 0 . 0 . . 124;139;100;112 7,5 0.0 1330 +0.3 1 GENE1 X - ref 0.333 0 1 0 . 0 . . 121;134;101;112 6,5 1195.0 1498 +0.4 2 GENE1 X - ref 0.333 1 . 1 . 1 . . 121;138;102;112 6,5 . 1470 +0.5 0 GENE1 X - ref 0.333 1 1 0 . 0 . . 121;139;100;112 6,5 1195.0 1450 +0.6 1 GENE1 X - ref 0.500 0 1 1 . 0 . . 100;110;60;89 5,1 869.0 1094 +0.7 0 GENE1 X - ref 0.500 1 1 1 . 0 . . 100;112;62;89 5,1 869.0 1125 +0.8 1 GENE1 X - ref 0.500 1 1 0 . 0 . . 100;110;76;84 5,3 0.0 1530 +0.9 0 GENE1 X - ref 0.500 0 1 0 . 0 . . 100;112;75;84 5,3 0.0 1527 +0.10 0 GENE1 X - ref 0.500 1 1 0 . 0 . . 75;90;48;63 4,0 665.0 1045 +0.11 1 GENE1 X - ref 0.500 0 1 0 . 0 . . 75;97;49;63 4,0 665.0 918 +0.12 0 GENE1 X - ref 0.500 0 . 0 . 1 . . 66;90;.;. 2,. . 1115 +0.13 1 GENE1 X - ref 0.500 1 . 1 . 1 . . 66;97;.;. 2,. . 930 diff --git a/tests/test1/test1neg/ref_peptides_gt.fa b/tests/test1/test1neg/ref_peptides_gt.fa new file mode 100644 index 00000000..e3f35cf3 --- /dev/null +++ b/tests/test1/test1neg/ref_peptides_gt.fa @@ -0,0 +1,28 @@ +>0.0 GENE1 +RTHDGLR +>0.1 GENE1 +MTHA +>0.2 GENE1 +DDARMMGCG +>0.3 GENE1 +RTHGDGLR +>0.4 GENE1 +MTHAW +>0.5 GENE1 +DDARMVMGCG +>0.6 GENE1 +GLRIQVRIVAK +>0.7 GENE1 +MGCGFRYV +>0.8 GENE1 +GLRSTY +>0.9 GENE1 +MGCGVRI +>0.10 GENE1 +VQVRISTFWW +>0.11 GENE1 +SSSSGTYIDVLV +>0.12 GENE1 +VQVRIVAK +>0.13 GENE1 +SSSSGTYSC diff --git a/tests/test1/test1neg/somatic_and_germline_metadata.tsv.gz b/tests/test1/test1neg/somatic_and_germline_metadata.tsv.gz new file mode 100644 index 00000000..820bbe7c Binary files /dev/null and b/tests/test1/test1neg/somatic_and_germline_metadata.tsv.gz differ diff --git a/tests/test1/test1neg/somatic_and_germline_metadata_gt.tsv b/tests/test1/test1neg/somatic_and_germline_metadata_gt.tsv new file mode 100644 index 00000000..2992b50c --- /dev/null +++ b/tests/test1/test1neg/somatic_and_germline_metadata_gt.tsv @@ -0,0 +1,9 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 1 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 124;134;101;112 7,5 0.0 1351 +0.1 2 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 124;138;102;112 7,5 0.0 1338 +0.2 0 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 124;139;100;112 7,5 0.0 1330 +0.3 1 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 121;134;101;112 6,5 1195.0 1498 +0.4 2 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 121;138;102;112 6,5 1195.0 1470 +0.5 0 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 121;139;100;112 6,5 1195.0 1450 +0.6 0 GENE1 X - somatic_and_germline 0.333 0 1 1 . 0 111 1409 100;112;62;89 5,1 869.0 1125 +0.7 0 GENE1 X - somatic_and_germline 0.333 0 1 0 . 0 111 1409 100;112;75;84 5,3 0.0 1527 diff --git a/tests/test1/test1neg/somatic_and_germline_peptides_gt.fa b/tests/test1/test1neg/somatic_and_germline_peptides_gt.fa new file mode 100644 index 00000000..2a141ded --- /dev/null +++ b/tests/test1/test1neg/somatic_and_germline_peptides_gt.fa @@ -0,0 +1,16 @@ +>0.0 GENE1 +RTHGGLR +>0.1 GENE1 +ITHAWWVA +>0.2 GENE1 +DHARMVGCG +>0.3 GENE1 +RTHGGGLR +>0.4 GENE1 +ITHAWWWVA +>0.5 GENE1 +DHARMVVGCG +>0.6 GENE1 +VGCGFRYV +>0.7 GENE1 +VGCGVRI diff --git a/tests/test1/test1neg/somatic_metadata.tsv.gz b/tests/test1/test1neg/somatic_metadata.tsv.gz new file mode 100644 index 00000000..2210800d Binary files /dev/null and b/tests/test1/test1neg/somatic_metadata.tsv.gz differ diff --git a/tests/test1/test1neg/somatic_metadata_gt.tsv b/tests/test1/test1neg/somatic_metadata_gt.tsv new file mode 100644 index 00000000..9cc13bdd --- /dev/null +++ b/tests/test1/test1neg/somatic_metadata_gt.tsv @@ -0,0 +1,9 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 1 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 124;134;101;112 7,5 0.0 1351 +0.1 2 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 124;138;102;112 7,5 0.0 1338 +0.2 0 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 124;139;100;112 7,5 0.0 1330 +0.3 1 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 121;134;101;112 6,5 1195.0 1498 +0.4 2 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 121;138;102;112 6,5 1195.0 1470 +0.5 0 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 121;139;100;112 6,5 1195.0 1450 +0.6 0 GENE1 X - somatic 0.333 0 1 1 . 0 111 1409 100;112;62;89 5,1 869.0 1125 +0.7 0 GENE1 X - somatic 0.333 0 1 0 . 0 111 1409 100;112;75;84 5,3 0.0 1527 diff --git a/tests/test1/test1neg/somatic_peptides_gt.fa b/tests/test1/test1neg/somatic_peptides_gt.fa new file mode 100644 index 00000000..a729b503 --- /dev/null +++ b/tests/test1/test1neg/somatic_peptides_gt.fa @@ -0,0 +1,16 @@ +>0.0 GENE1 +RTHGGLR +>0.1 GENE1 +MTHAWWVA +>0.2 GENE1 +DDARMVGCG +>0.3 GENE1 +RTHGGGLR +>0.4 GENE1 +MTHAWWWVA +>0.5 GENE1 +DDARMVVGCG +>0.6 GENE1 +VGCGFRYV +>0.7 GENE1 +VGCGVRI diff --git a/tests/test1/test1pos/germline_metadata.tsv.gz b/tests/test1/test1pos/germline_metadata.tsv.gz new file mode 100644 index 00000000..ea55f72e Binary files /dev/null and b/tests/test1/test1pos/germline_metadata.tsv.gz differ diff --git a/tests/test1/test1pos/germline_metadata_gt.tsv b/tests/test1/test1pos/germline_metadata_gt.tsv new file mode 100644 index 00000000..fbee26ad --- /dev/null +++ b/tests/test1/test1pos/germline_metadata_gt.tsv @@ -0,0 +1,5 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 0 GENE1 X + germline 0.333 0 1 0 . 0 . . 11;26;38;50 0,2 0.0 1330 +0.1 2 GENE1 X + germline 0.333 1 . 1 . 1 . . 12;26;38;48 0,2 . 1338 +0.2 0 GENE1 X + germline 0.333 1 1 0 . 0 . . 11;29;38;50 1,2 1195.0 1450 +0.3 2 GENE1 X + germline 0.333 1 . 1 . 1 . . 12;29;38;48 1,2 . 1470 diff --git a/tests/test1/test1pos/germline_peptides_gt.fa b/tests/test1/test1pos/germline_peptides_gt.fa new file mode 100644 index 00000000..1bb8d5e7 --- /dev/null +++ b/tests/test1/test1pos/germline_peptides_gt.fa @@ -0,0 +1,8 @@ +>0.0 GENE1 +DHARMMGCG +>0.1 GENE1 +ITHA +>0.2 GENE1 +DHARMVMGCG +>0.3 GENE1 +ITHAW diff --git a/tests/test1/test1pos/ref_metadata.tsv.gz b/tests/test1/test1pos/ref_metadata.tsv.gz new file mode 100644 index 00000000..2f07e275 Binary files /dev/null and b/tests/test1/test1pos/ref_metadata.tsv.gz differ diff --git a/tests/test1/test1pos/ref_metadata_gt.tsv b/tests/test1/test1pos/ref_metadata_gt.tsv new file mode 100644 index 00000000..377c4f41 --- /dev/null +++ b/tests/test1/test1pos/ref_metadata_gt.tsv @@ -0,0 +1,15 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 0 GENE1 X + ref 0.333 0 1 0 . 0 . . 11;26;38;50 0,2 0.0 1330 +0.1 2 GENE1 X + ref 0.333 1 . 1 . 1 . . 12;26;38;48 0,2 . 1338 +0.2 1 GENE1 X + ref 0.333 1 1 0 . 0 . . 16;26;38;49 0,2 0.0 1351 +0.3 0 GENE1 X + ref 0.333 1 1 0 . 0 . . 11;29;38;50 1,2 1195.0 1450 +0.4 2 GENE1 X + ref 0.333 1 . 1 . 1 . . 12;29;38;48 1,2 . 1470 +0.5 1 GENE1 X + ref 0.333 0 1 0 . 0 . . 16;29;38;49 1,2 1195.0 1498 +0.6 0 GENE1 X + ref 0.500 1 1 1 . 0 . . 38;50;61;88 2,5 869.0 1125 +0.7 1 GENE1 X + ref 0.500 0 1 1 . 0 . . 40;50;61;90 2,5 869.0 1094 +0.8 0 GENE1 X + ref 0.500 0 1 0 . 0 . . 38;50;66;75 2,6 0.0 1527 +0.9 1 GENE1 X + ref 0.500 1 1 0 . 0 . . 40;50;66;74 2,6 0.0 1530 +0.10 1 GENE1 X + ref 0.500 0 1 0 . 0 . . 53;75;87;101 3,7 665.0 918 +0.11 0 GENE1 X + ref 0.500 1 1 0 . 0 . . 60;75;87;102 3,7 665.0 1045 +0.12 1 GENE1 X + ref 0.500 1 . 1 . 1 . . 53;84;.;. 4,. . 930 +0.13 0 GENE1 X + ref 0.500 0 . 0 . 1 . . 60;84;.;. 4,. . 1115 diff --git a/tests/test1/test1pos/ref_peptides_gt.fa b/tests/test1/test1pos/ref_peptides_gt.fa new file mode 100644 index 00000000..bc9fd079 --- /dev/null +++ b/tests/test1/test1pos/ref_peptides_gt.fa @@ -0,0 +1,28 @@ +>0.0 GENE1 +DDARMMGCG +>0.1 GENE1 +MTHA +>0.2 GENE1 +RTHDGLR +>0.3 GENE1 +DDARMVMGCG +>0.4 GENE1 +MTHAW +>0.5 GENE1 +RTHGDGLR +>0.6 GENE1 +MGCGFRYV +>0.7 GENE1 +GLRIQVRIVAK +>0.8 GENE1 +MGCGVRI +>0.9 GENE1 +GLRSTY +>0.10 GENE1 +SSSSGTYIDVLV +>0.11 GENE1 +VQVRISTFWW +>0.12 GENE1 +SSSSGTYSC +>0.13 GENE1 +VQVRIVAK diff --git a/tests/test1/test1pos/somatic_and_germline_metadata.tsv.gz b/tests/test1/test1pos/somatic_and_germline_metadata.tsv.gz new file mode 100644 index 00000000..64c8b8af Binary files /dev/null and b/tests/test1/test1pos/somatic_and_germline_metadata.tsv.gz differ diff --git a/tests/test1/test1pos/somatic_and_germline_metadata_gt.tsv b/tests/test1/test1pos/somatic_and_germline_metadata_gt.tsv new file mode 100644 index 00000000..9a41e50e --- /dev/null +++ b/tests/test1/test1pos/somatic_and_germline_metadata_gt.tsv @@ -0,0 +1,9 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 0 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 11;26;38;50 0,2 0.0 1330 +0.1 2 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 12;26;38;48 0,2 0.0 1338 +0.2 1 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 16;26;38;49 0,2 0.0 1351 +0.3 0 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 11;29;38;50 1,2 1195.0 1450 +0.4 2 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 12;29;38;48 1,2 1195.0 1470 +0.5 1 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 16;29;38;49 1,2 1195.0 1498 +0.6 0 GENE1 X + somatic_and_germline 0.333 0 1 1 . 0 38 1409 38;50;61;88 2,5 869.0 1125 +0.7 0 GENE1 X + somatic_and_germline 0.333 0 1 0 . 0 38 1409 38;50;66;75 2,6 0.0 1527 diff --git a/tests/test1/test1pos/somatic_and_germline_peptides_gt.fa b/tests/test1/test1pos/somatic_and_germline_peptides_gt.fa new file mode 100644 index 00000000..7ef972c2 --- /dev/null +++ b/tests/test1/test1pos/somatic_and_germline_peptides_gt.fa @@ -0,0 +1,16 @@ +>0.0 GENE1 +DHARMVGCG +>0.1 GENE1 +ITHAWWVA +>0.2 GENE1 +RTHGGLR +>0.3 GENE1 +DHARMVVGCG +>0.4 GENE1 +ITHAWWWVA +>0.5 GENE1 +RTHGGGLR +>0.6 GENE1 +VGCGFRYV +>0.7 GENE1 +VGCGVRI diff --git a/tests/test1/test1pos/somatic_metadata.tsv.gz b/tests/test1/test1pos/somatic_metadata.tsv.gz new file mode 100644 index 00000000..5f6098e9 Binary files /dev/null and b/tests/test1/test1pos/somatic_metadata.tsv.gz differ diff --git a/tests/test1/test1pos/somatic_metadata_gt.tsv b/tests/test1/test1pos/somatic_metadata_gt.tsv new file mode 100644 index 00000000..adfbb17c --- /dev/null +++ b/tests/test1/test1pos/somatic_metadata_gt.tsv @@ -0,0 +1,9 @@ +output_id read_frame gene_name gene_chr gene_strand mutation_mode peptide_weight peptide_annotated junction_annotated has_stop_codon is_in_junction_list is_isolated variant_comb variant_seg_expr exons_coor vertex_idx junction_expr segment_expr +0.0 0 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 11;26;38;50 0,2 0.0 1330 +0.1 2 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 12;26;38;48 0,2 0.0 1338 +0.2 1 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 16;26;38;49 0,2 0.0 1351 +0.3 0 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 11;29;38;50 1,2 1195.0 1450 +0.4 2 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 12;29;38;48 1,2 1195.0 1470 +0.5 1 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 16;29;38;49 1,2 1195.0 1498 +0.6 0 GENE1 X + somatic 0.333 0 1 1 . 0 38 1409 38;50;61;88 2,5 869.0 1125 +0.7 0 GENE1 X + somatic 0.333 0 1 0 . 0 38 1409 38;50;66;75 2,6 0.0 1527 diff --git a/tests/test1/test1pos/somatic_peptides_gt.fa b/tests/test1/test1pos/somatic_peptides_gt.fa new file mode 100644 index 00000000..26184d65 --- /dev/null +++ b/tests/test1/test1pos/somatic_peptides_gt.fa @@ -0,0 +1,16 @@ +>0.0 GENE1 +DDARMVGCG +>0.1 GENE1 +MTHAWWVA +>0.2 GENE1 +RTHGGLR +>0.3 GENE1 +DDARMVVGCG +>0.4 GENE1 +MTHAWWWVA +>0.5 GENE1 +RTHGGGLR +>0.6 GENE1 +VGCGFRYV +>0.7 GENE1 +VGCGVRI diff --git a/tests/test_end_to_end.py b/tests/test_end_to_end.py new file mode 100644 index 00000000..a8e33a59 --- /dev/null +++ b/tests/test_end_to_end.py @@ -0,0 +1,66 @@ +import gzip +import os + +import pytest + + +data_dir = os.path.join(os.path.dirname(__file__), 'data') +sample_dir = os.path.join(os.path.dirname(__file__), 'test1') +from immunopepper import main_immuno + + +def _assert_files_equal(expected_path, actual_path): + def o(f): + if f.endswith('.gz'): + return gzip.open(f, 'rb') + else: + return open(f, 'r') + + with o(expected_path) as e: + with o(actual_path) as a: + assert e.read() == a.read() + + + +@pytest.mark.parametrize("test_id,case,mutation_mode", [ + ['1', 'pos', 'ref'], + ['1', 'pos', 'germline'], + ['1', 'pos', 'somatic'], + ['1', 'pos', 'somatic_and_germline'], + ['1', 'neg', 'ref'], + ['1', 'neg', 'germline'], + ['1', 'neg', 'somatic'], + ['1', 'neg', 'somatic_and_germline'] +]) + + +def test_end_to_end_ref(test_id, case, mutation_mode, tmpdir): + data_dir = os.path.join(os.path.dirname(__file__), 'test{}'.format(test_id), 'data') + sample_dir = os.path.join(os.path.dirname(__file__), 'test{}'.format(test_id), 'test{}{}'.format(test_id,case)) + + out_dir = str(tmpdir) + + my_args = ['--samples', 'test{}{}'.format(test_id,case), + '--output_dir', out_dir, + '--splice_path', + '{}/{}graph/spladder/genes_graph_conf3.merge_graphs.pickle'.format( + data_dir, case), + '--count_path', + '{}/{}graph/spladder/genes_graph_conf3.merge_graphs.count.hdf5'.format( + data_dir, case), + '--ann_path', '{}/test{}{}.gtf'.format(data_dir, test_id, case), + '--ref_path', '{}/test{}{}.fa'.format(data_dir, test_id, case), + '--vcf_path', '{}/test{}{}.vcf'.format(data_dir, test_id, case), + '--maf_path', '{}/test{}{}.maf'.format(data_dir, test_id, case), + '--mutation_mode', mutation_mode, + '--filter_redundant'] + + main_immuno.main(main_immuno.parse_arguments(my_args)) + + _assert_files_equal( + os.path.join(sample_dir, '{}_peptides_gt.fa'.format(mutation_mode)), + os.path.join(out_dir, 'test{}{}'.format(test_id, case), '{}_peptides.fa'.format(mutation_mode))) + + _assert_files_equal( + os.path.join(sample_dir, '{}_metadata_gt.tsv'.format(mutation_mode)), + os.path.join(out_dir, 'test{}{}'.format(test_id, case), '{}_metadata.tsv.gz'.format(mutation_mode))) diff --git a/tests/test_immunopepper.py b/tests/test_immunopepper.py index e69de29b..7e28fa79 100644 --- a/tests/test_immunopepper.py +++ b/tests/test_immunopepper.py @@ -0,0 +1,160 @@ +import gzip +import os +import pickle + +import Bio.SeqIO as BioIO +import pytest + +from immunopepper.immuno_mutation import apply_germline_mutation,construct_mut_seq_with_str_concat,get_mutation_mode_from_parser +from immunopepper.immuno_preprocess import preprocess_ann, genes_preprocess, \ + parse_mutation_from_vcf, parse_mutation_from_maf +from immunopepper.utils import get_sub_mut_dna +from immunopepper.io_utils import load_pickled_graph +from immunopepper.main_immuno import parse_arguments + +data_dir = os.path.join(os.path.dirname(__file__), 'test1','data') + + +@pytest.fixture +def load_gene_data(): + f = open(os.path.join(data_dir, 'posgraph','spladder', + 'genes_graph_conf3.merge_graphs.pickle'), 'r') + ann_path = os.path.join(data_dir, 'test1pos.gtf') + ref_path = os.path.join(data_dir, 'test1pos.fa') + + (graph_data, graph_meta) = load_pickled_graph(f) # cPickle.load(f) + genetable = preprocess_ann(ann_path) + interesting_chr = map(str, range(1, 23)) + ["X", "Y", "MT"] + seq_dict = {} + for record in BioIO.parse(ref_path, "fasta"): + if record.id in interesting_chr: + seq_dict[record.id] = str(record.seq).strip() + + gene = graph_data[0] + chrm = gene.chr.strip() + ref_seq = seq_dict[chrm] + return graph_data, ref_seq, genetable.gene_to_cds_begin + + +@pytest.fixture +def load_mutation_data(): + vcf_path = os.path.join(data_dir, 'test1pos.vcf') + maf_path = os.path.join(data_dir, 'test1pos.maf') + mutation_dic_vcf = parse_mutation_from_vcf(vcf_path,['test1pos']) + mutation_dic_maf = parse_mutation_from_maf(maf_path) + + return mutation_dic_vcf, mutation_dic_maf + + +def test_preprocess(load_gene_data): + graph_data, seq_dict, gene_cds_begin_dict = load_gene_data + genes_preprocess(graph_data, gene_cds_begin_dict) + assert graph_data[0].nvertices == 8 + + +def test_germline_mutation(load_gene_data, load_mutation_data): + graph_data, ref_seq, gene_cds_begin_dict = load_gene_data + mutation_dic_vcf, mutation_dic_maf = load_mutation_data + gene = graph_data[0] + mutation_sub_dic_vcf = mutation_dic_vcf['test1pos', gene.chr] + ref_mut_seq = apply_germline_mutation(ref_sequence=ref_seq, + pos_start=gene.start, + pos_end=gene.stop, + mutation_sub_dic_vcf=mutation_sub_dic_vcf) + assert 'ref' in ref_mut_seq.keys() + + +def test_get_sub_mut_dna(load_gene_data, load_mutation_data): + graph_data, ref_seq, gene_cds_begin_dict = load_gene_data + mutation_dic_vcf, mutation_dic_maf = load_mutation_data + gene = graph_data[0] + + # made modification to the mutation_dic_vcf + var_dict = {'ref_base': 'G', 'mut_base': 'A', 'strand': '+', + 'Variant_Classification': 'Silent', 'Variant_Type': 'SNP'} + mutation_sub_dic_maf = mutation_dic_maf['test1pos', gene.chr] + mutation_sub_dic_maf[41] = var_dict + test_list = [[11, 29, 38, 50], + [11, 29, 38, 50], + [60, 75, 87, 102]] + groundtruth = ['GATGACGCACGCATGGTGGTGGGTTGCGGA', + 'GATGACGCACGCATGGTGGTGAGTTGCGGA', + 'GTTCAGGTACGTATATCGACGTTCTGGTGG', + ] + variant_comb = [(38,), (38, 41), '.'] + strand = ['+', '+', '+'] + for i, vlist in enumerate(test_list): + sub_dna = get_sub_mut_dna(ref_seq, vlist[0], vlist[1], vlist[2], + vlist[3], variant_comb[i], + mutation_sub_dic_maf, strand[i]) + assert sub_dna == groundtruth[i] + + +def test_reading_gtf_and_gff3_file(): + gff3_path = os.path.join(data_dir,'small.gencode.v29.gff3') + gtf_path = os.path.join(data_dir, 'small.gencode.v29.gtf') + gene_table_gtf = preprocess_ann(gtf_path) + gene_table_gff = preprocess_ann(gff3_path) + assert gene_table_gff.gene_to_ts == gene_table_gtf.gene_to_ts + assert gene_table_gtf.ts_to_cds.keys() == gene_table_gff.ts_to_cds.keys() + assert gene_table_gtf.ts_to_cds['ENST00000335137.4'] == [(69090, 70004, 0)] + assert gene_table_gff.ts_to_cds['ENST00000335137.4'] == [(69090, 70007, 0)] # include stop codon in gff3 + + +def test_reading_gtf_and_gff_file(): + gff_path = os.path.join(data_dir,'small.gencode.v19.gff') + gtf_path = os.path.join(data_dir, 'small.gencode.v19.gtf') + gene_table_gtf = preprocess_ann(gtf_path) + gene_table_gff = preprocess_ann(gff_path) + assert gene_table_gff.gene_to_ts == gene_table_gtf.gene_to_ts + assert gene_table_gtf.ts_to_cds.keys() == gene_table_gff.ts_to_cds.keys() + assert gene_table_gff.ts_to_cds['ENST00000335137.3'] == [(69090, 70005, 0)] + assert gene_table_gtf.ts_to_cds['ENST00000335137.3'] == [(69090, 70004, 0)] + + +def test_reading_vcf_h5(): + vcf_dict_default_heter_code0 = parse_mutation_from_vcf(os.path.join(data_dir,'test1vcf.h5'),['test1pos','test1neg']) + vcf_dict_heter_code2 = parse_mutation_from_vcf(os.path.join(data_dir,'test1vcf.h5'),['test1pos','test1neg'],heter_code=2) + assert len(vcf_dict_default_heter_code0) == 2 + assert vcf_dict_default_heter_code0['test1neg', 'X'][135] == {'mut_base': 'G', 'ref_base': 'C'} + assert vcf_dict_default_heter_code0['test1pos', 'X'][14] == {'mut_base': 'C', 'ref_base':'G'} + assert vcf_dict_heter_code2['test1pos', 'X'][135] == {'mut_base': 'G', 'ref_base': 'C'} + assert vcf_dict_heter_code2['test1neg', 'X'][14] == {'mut_base': 'C', 'ref_base':'G'} + assert vcf_dict_heter_code2['test1neg', 'X'][135] == {'mut_base': 'G', 'ref_base':'C'} + + +def test_construct_mut_seq_with_str_concat(): + ref_seq = 'GTAATGTGTAAGATGACGCACGCATGGTGGTATTGGAGATGGGTTGCGGAGTAAGTTCGAGTTC' + gt_mut_seq1 = 'GTAATGTGTAGGATGACGCACGCATACTGGTATTGGAGATGGTTTGCGGAGTAAGTTCGAGTTC' + gt_mut_seq2 = 'GTAATGTGTAAGATGACGCACGCATGCTGGTATTGGAGATGGGTTGCGGAGTAAGTTCGAGTTC' + mut_dict = {} + mut_dict[10] = {'mut_base':'G','ref_base':'A'} + mut_dict[25] = {'mut_base':'A','ref_base':'G'} + mut_dict[26] = {'mut_base':'C','ref_base':'G'} + mut_dict[28] = {'mut_base':'*','ref_base':'G'} + mut_dict[42] = {'mut_base':'T','ref_base':'G'} + mut_dict[45] = {'mut_base':'*','ref_base':'G'} + mut_seq1 = construct_mut_seq_with_str_concat(ref_seq,0,len(ref_seq),mut_dict) + assert mut_seq1 == gt_mut_seq1 + mut_seq2 = construct_mut_seq_with_str_concat(ref_seq,25,27,mut_dict) # (25,27) open in two side, only include 26 + assert mut_seq2 == gt_mut_seq2 + mut_seq3 = construct_mut_seq_with_str_concat(ref_seq,25,26,mut_dict) + assert mut_seq3 == ref_seq + + +def test_get_mutation_mode_from_parser(): + my_args1 = ['--vcf_path', os.path.join(data_dir,'test1pos.vcf'), + '--maf_path', os.path.join(data_dir,'test1pos.maf'), + '--mutation_mode', 'somantic'] # bad mutation mode + args = parse_arguments(my_args1) + try: + get_mutation_mode_from_parser(args) + except SystemExit: + assert 1 + my_args2 = ['--vcf_path', os.path.join(data_dir,'test1pos.vcf'), + '--mutation_mode', 'somatic'] # mismatch mutation mode and input files + args = parse_arguments(my_args2) + try: + get_mutation_mode_from_parser(args) + except SystemExit: + assert 1 diff --git a/tox.ini b/tox.ini index 32a99653..6adf2146 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,9 @@ [tox] ; could add some more environments in the future -envlist = py27, py36, flake8 +envlist = py27, flake8 [travis] python = - 3.6: py36 - 3.5: py35 - 3.4: py34 2.7: py27 [testenv:flake8]