Merge pull request #28 from sbslee/0.7.0-dev

0.7.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,31 @@
 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)
 ------------------
 
@@ -45,10 +70,10 @@ Changelog
 * 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)
 ------------------

README.rst

@@ -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``
@@ -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``.
@@ -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
 ============
@@ -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.