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Testing Instructions

The following outlines testing protocols for each active tool in the wiki. These tests are not comprehensive, but represent the typical input/output done by most of the researchers which use these tools. Test data supplied by the CfE research team.

Sequencing layout designer

See sequencing_layout/Sequencing_Layout_template.xlsx for an example of data to be used with this tool. Copy the Sample ID column (8 rows) into the leftmost text box and the Primer column (8 rows) into the middle text box.

Complete the User Information fields, using some <your_test> identifier for Plate ID. Then press Populate, followed by Update FROM table. Leave Horizontal selected in Layout Parameters. Then press Submit. You should recieve an email with two files: <your_test>.plt and <your_test>.html.

The output file data should match sequencing_layout/sequencing_output.plt and sequencing_layout/sequencing_output.html.

Guava layout designer

Fill the leftmost table with

ctrl1
ctrl2
ctrl3
ctrl4
ctrl5
ctrl6
ctrl7
ctrl8

And the center table with

samp1
samp2
samp3
samp4
samp5
samp6
samp7
samp8

Instructions will be in the rightmost table. Using default settings, with ExperimentID=<your_test>, press Populate, followed by Update FROM table. Then press Submit. You should recieve an email with two files: <your_test>.csv and <your_test>.html.

The output file data should match guava_layout/guava_output.csv and guava_layout/guava_output.html.

Fasta Converter

Upload or copy-and-paste the test.fasta file, and you should get a CSV file that matches fasta_converter/converted.csv.

NOTE: the CSV-to-Fasta conversion currently has an issue, which is open in this repo.

Text-to-Columns

Copy-and-paste the contents of text_to_columns/ttc_input.csv, and you should be able to download a file which matches text_to_columns/ttc_output.csv.

NOTE: there is an issue in the current version - if each row in the input file is not the same length the result will be a 500 Server Error message. This is fixed in the test branch, as seen here: #2

False discovery q-value

This tool does not need a test input file. By default, the following values are populated in the text field:

0.51
0.01
0.12
0.16
0.92
0.16
0.01
0.51
0.62

The output file is located in qvalue/q-values_output.xlsx

HXB2 Genome map

No testing should be needed. The page will load, or it won't. The contents shouldn't change.

A copy of the HTML page is located in HIV_genome/HIV-I HXB2 Genome.html.

DNA translator

Copy-and-paste the input file translate_DNA/test_translate_DNA.fasta into the text field, with the default settings, and you should get the output found in translate_DNA/test_translate_DNA_output.txt.

Quality Check

The test.fasta file, with all analysis entries checked (default), should produce an output file which matches quality_check/quality_check_data_test.xlsx.

Unique Sequence Finder

The test.fasta file should produce an output file identical to unique_sequence/unique_sequence_data_noduplicate.csv.

The unique_sequence/test_duplicate.fasta file should match unique_sequence/unique_sequence_data_duplicate.csv.

Variable function analyzer - doesn't need test data, but save output file

This tool does not need test input data. To test, the following values in the page text should be copied into the text input field:

A02:26	A03:01:01G	B07:02:01G	B40:01:01G	C03:04:01G	C07:02:01G	0.3
A01:01:01G	A02:01:01G	B08:01:01G	B15:01:01G	C03:04:01G	C07:01:01G	0.7
A01:01:01G	A02:01:01G	B08:01:01G	B57:01:01G	C06:02:01G	C07:01:01G	0.8
A02:01:01G	A03:01:01G	B14:02:01	B15:34	C03:04:01G	C08:02:01	0.3
A02:01:01G	A24:03:01G	B38:01:01	B51:01:01G	C12:03:01G	C14:02:01	0.45
A02:01:01G	A02:01:01G	B14:02:01	B40:01:01G	C03:04:01G	C08:02:01	0.3
A01:01:01G	A01:01:01G	B08:01:01G	B57:01:01G	C06:02:01G	C07:01:01G	0.75
A11:01:01G	A23:01:01G	B07:02:01G	B51:01:01G	C04:01:01G	C15:02:01G	0.2
A01:01:01G	A03:01:01G	B27:05:02G	B57:01:01G	C01:02:01G	C06:02:01G	0.8
A01:01:01G	A02:01:01G	B08:01:01G	B44:02:01G	C02:02:02G	C07:01:01G	0.7
A01:01:01G	A11:01:01G	B08:01:01G	B35:01:01G	C04:01:01G	C07:64	0.9
A02:01:01G	A24:02:01G	B15:01:01G	B15:07:01G	C01:02:01G	C03:03:01G	0.4
A01:01:01G	A25:01:01G	B08:01:01G	B39:01:01G	C07:01:01G	C12:03:01G	0.6

The output file is located in variable_function/variable_function_output.csv

Codon-by-Codon

This tool does not need a test input file. By default, the following values are populated in the text field:

0.786	MGGKWSKRNVVEWPTVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTATNNAACAWLEAQEEEEVGFPVRPQVPLRPMTYRAAVDLSHFLKEKGGLGGLIHSQKRQDILDLWVYHTQGYFPDWQNYTPGPGIRYPLCFGWCFKLVPVEPDKVEEANEGENNSLLHPMSLHGMEDPEGEVLMWKFDSRLAFHHMARELHPEYYKDC
0.982	MGGKWSKSSMVGWPKVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQEDEEVGFPVRPQVPLRPMTYKAAIDLSHFLKEKGGLEGLIYSQKRQDILDLWVYHTQGFFPDWQNYTPGPGVRYPLTFGWCFKLVPVDPEKVEEANEGENNSLLHPMSLHGMEDTEKEVLAWRFDSLLAFRHMAREVHPEYYKDC
1.021	MGSKWSKSSVVGWPDVRERMRRAEPAADGVGAVSRDLERHGAITSGNTATNNADCAWLEAQEDEEVGFPVRPQVPLRPMTHRAAMDLSHFLRDKGGLDGLIWSQKRQDILDLWVYHTQGFFPDWQNYTPGPGTRFPLTFGWCFKLVPVELEKVEEANEGENNSLLHPMSQHGMEDPEKEVLAWRFDSRLAFQHMARELHPEYYKDC
0.214	MGGKWSKCSTPGWSTIRERMRRAEPAADGVGPASRDLEKHGALTSSNTAANNAACAWLEAQEEEEVGFPVRPQVPLRPMTYKGALDLSHFLNEKGGLEGLIYSQKRQDILDLWVYNTQGFFPDWQNYTPGPGVRYPLCFGWCFKLVPVESEKVEEATEGENNSLLHPVCLHGMDDPEGEVLVWKFDSKLAFHHMAREMHPEYYKNC
0.467	MGGKWSKCSMGGWPSVRERMRRTEPAAEGVGAASRDLERHGALTSNNTPTNNAACAWLEAQEEEEVGFPVRPQVPLRPMTYKGALDLSHFLKEKGGLEGLVYSQKRQDILDLWVFNTQGFFPDWQGYTPGPGIRYPLTFGWCFKLVPMEPDKVEEANEGENNSLLHPVSLHGMEDPEREVLVWRFDSRLAFRHVAQELHPEYYKNR
0.801	MGGKWSKLS--GWHTIRERMRRAEPAADGVGATSRDLERHGAVTSSNTATNNGACARPEAQENDEVGFPVRPQVPLRPMTFKAAFDLSHFLKEKGGLDGLVYSQKRQEILDLWVYHTQGYLPDWQNYTPGPGTRYPLCFGWCFKLVPMEQEKVEEANEGENNRLLHPISQHGMEDPEREVLVWKFDSSLAFHHRARELHPEFYKDC

The output should match the data in codon_by_codon/test_codon_by_codon.xlsx.

Phylodating

Testing instructions for this tool are thoroughly described on the Phylodating page.

HLA Class(ification Tool)

Use test.fasta for this tool, in Batch Mode, with HLA Locus: C.

The results should match hla_class/HLA-C batch mode test data OUTPUT.csv.

If you select HLA Locus: A or B, you should get an error message about invalid sequences (or if in Single Sequence Mode, about the length of the sequences.)

PHAGE-I-Expanded

This tool does not need a test input file. Press Load Sample and select Gag as Protein of Interest.

The output TSV (tab separated values) file should match phage_i_expanded/phage_i_expanded_results_gag_test.tsv.

TCR Distance

There are two formats of input data, one is a "clones" file in TSV (tab separated values) format. The other is a pair of "annotations" files: consensus annotations, and filtered contig annotations. Both types are contained in subdirectories of tcr_distance/. Make sure to select human, not mouse.

These inputs should produce .dist files which match the output files in the corresponding subdirectories.

TCR Visualizer

The .dist files from the TCR Distance tool should be loadable in the TCR visualizer, and produce a network diagram. The number of edges can be altered by the Edge distance limit field, and the Sample report will tell you how many connected nodes are in the diagram.

There is no rigorous output file for testing, since this is a visualization sandbox tool.