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Merge pull request #28 from sbslee/0.7.0-dev
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0.7.0 dev
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@sbslee
sbslee authored Oct 23, 2021
2 parents 79c8d9d + 68e59af commit 1b0ec72
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27 changes: 26 additions & 1 deletion CHANGELOG.rst
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Changelog
*********

0.7.0 (2021-10-23)
------------------

* Fix minor bug in :meth:`api.core.predict_phenotype` when specified diplotype is not present in diplotype table.
* Dissolve **Database of Pharmacogenomic Structural Variants (DPSV)** page and move its SV data to **Genes** page.
* Add new method :meth:`api.core.get_variant_impact`.
* Update :meth:`api.utils.sort_alleles` method to give priority to alleles that impact protein coding when breaking ties (i.e. alleles have the same functional status and same number of variants).
* Update CNV caller for SLC22A2 and UGT2B15 genes.
* Rename ``--chr-prefix`` argument in :command:`create-regions-bed` to ``--add-chr-prefix``.
* Add ``--samples`` argument to :command:`run-ngs-pipeline` command.
* Add new command :command:`compare-genotypes`.
* Update :meth:`api.genotype.call_genotypes` method to assume the samples have no SV when CNV calls are not provided even if the target gene is known to have SV.
* Add new command :command:`run-chip-pipeline`.
* Fix minor bug in :command:`estimate-phase-beagle` command on not properly exiting the program even though there was an error raised by Beagle.
* Update :meth:`api.utils.create_consolidated_vcf` method to check synonymous variants as well when performing phase-extension algorithm.
* Update :command:`run-ngs-pipeline` command to output a warning when user provides CovFrame[DepthOfCoverage] even though target gene does not have any star alleles defined by SVs.
* Add new argument ``--fontsize`` argument to :command:`plot-bam-copy-number` command.
* Remove ``--ymin`` and ``--ymax`` arguments from :command:`plot-vcf-allele-fraction` command.
* Update ``--ymin`` and ``--ymax`` arguments of :command:`plot-bam-copy-number` command to have a default value.
* Add new command :command:`plot-cn-af`.
* Update :command:`run-ngs-pipeline` command to output a warning when user provides a VCF file even though target gene does not have any star alleles defined by SNVs/indels.
* Update aesthetics of copy number profile and allele fraction profile.
* Add new method :meth:`api.utils.count_alleles`.
* Update variant information for following alleles: CYP2A6\*35, UGT1A1\*28, UGT1A1\*37.

0.6.0 (2021-10-09)
------------------

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* Update :command:`create-consolidated-vcf` command to implement phase-extension algorithm.
* Remove ``SO`` and ``Type`` columns from the variant table.
* Update :class:`api.genotype.GSTM1Genotyper` class.
* Update variant information for following alleles: CYP1A2\*1C, CYP1A2\*1F, CYP1A2\*1K, CYP1A2\*1L, CYP2B6\*17, CYP2D6\*15, CYP2D6\*21, SLCO1B1\*S1, SLCO1B1\*S2.
* Add ``NotTargetGeneError`` error.
* Add new method ``api.utils.is_target_gene``.
* Update :command:`run-ngs-pipeline` command to check whether input gene is one of the target genes before attempting to run the pipeline.
* Update variant information for following alleles: CYP1A2\*1C, CYP1A2\*1F, CYP1A2\*1K, CYP1A2\*1L, CYP2B6\*17, CYP2D6\*15, CYP2D6\*21, SLCO1B1\*S1, SLCO1B1\*S2.

0.4.1 (2021-09-21)
------------------
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31 changes: 17 additions & 14 deletions README.rst
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Expand Up @@ -101,8 +101,8 @@ In order to efficiently store and transfer data, PyPGx uses the ZIP archive file
- Target gene.
- ``CYP2D6``, ``GSTT1``
* - ``Platform``
- NGS platform.
- ``WGS``, ``Targeted``
- Genotyping platform.
- ``WGS``, ``Targeted``, ``Chip``
* - ``Program``
- Name of the phasing program.
- ``Beagle``
Expand All @@ -129,7 +129,7 @@ Notably, all archive files have defined semantic types, which allows us to ensur
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``, ``Control``.
- ``SampleTable[Alleles]``
* TSV file for storing target gene's candidate star alleles for each sample.
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.
* Requires following metadata: ``Platform``, ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.
- ``SampleTable[CNVCalls]``
* TSV file for storing target gene's CNV call for each sample.
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``, ``Control``.
Expand All @@ -147,13 +147,13 @@ Notably, all archive files have defined semantic types, which allows us to ensur
* Requires following metadata: ``Control``, ``Assembly``, ``SemanticType``, ``Platform``.
- ``VcfFrame[Consolidated]``
* VcfFrame for storing target gene's consolidated variant data.
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.
* Requires following metadata: ``Platform``, ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.
- ``VcfFrame[Imported]``
* VcfFrame for storing target gene's raw variant data.
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``.
* Requires following metadata: ``Platform``, ``Gene``, ``Assembly``, ``SemanticType``.
- ``VcfFrame[Phased]``
* VcfFrame for storing target gene's phased variant data.
* Requires following metadata: ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.
* Requires following metadata: ``Platform``, ``Gene``, ``Assembly``, ``SemanticType``, ``Program``.

Getting help
============
Expand All @@ -169,37 +169,40 @@ For getting help on the CLI:
positional arguments:
COMMAND
call-genotypes Call genotypes for target gene.
call-genotypes Call genotypes for the target gene.
call-phenotypes Call phenotypes for the target gene.
combine-results Combine various results for the target gene.
compare-genotypes Calculate concordance rate between two genotype results.
compute-control-statistics
Compute various statistics for control gene with BAM data.
Compute summary statistics for the control gene from BAM files.
compute-copy-number
Compute copy number from read depth for target gene.
Compute copy number from read depth for the target gene.
compute-target-depth
Compute read depth for target gene with BAM data.
Compute read depth for the target gene from BAM files.
create-consolidated-vcf
Create consolidated VCF.
Create a consolidated VCF file.
create-regions-bed Create a BED file which contains all regions used by PyPGx.
estimate-phase-beagle
Estimate haplotype phase of observed variants with the Beagle program.
filter-samples Filter Archive file for specified samples.
import-read-depth Import read depth data for target gene.
import-variants Import variant data for the target gene.
plot-bam-copy-number
Plot copy number profile with BAM data.
Plot copy number profile from CovFrame[CopyNumber].
plot-bam-read-depth
Plot read depth profile with BAM data.
plot-cn-af Plot both copy number profile and allele fraction profile in one figure.
plot-vcf-allele-fraction
Plot allele fraction profile with VCF data.
plot-vcf-read-depth
Plot read depth profile with VCF data.
predict-alleles Predict candidate star alleles based on observed variants.
predict-cnv Predict CNV for target gene based on copy number data.
predict-cnv Predict CNV for the target gene based on copy number data.
prepare-depth-of-coverage
Prepare a depth of coverage file for all target genes with SV.
print-metadata Print the metadata of specified archive.
run-ngs-pipeline Run NGS pipeline for the target gene.
run-chip-pipeline Run PyPGx's genotyping pipeline for chip data.
run-ngs-pipeline Run PyPGx's genotyping pipeline for NGS data.
test-cnv-caller Test a CNV caller for the target gene.
train-cnv-caller Train a CNV caller for the target gene.
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