Merge pull request #79 from sbslee/0.20.0-dev

0.20.0 dev

Author: sbslee

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Changelog
 *********
 
+0.20.0 (2023-01-12)
+-------------------
+
+* :issue:`73`: Fix bug in :command:`run-ngs-pipeline` command where empty VCF (i.e. no variants were found in the target gene) was causing error when plotting allele fraction. From now on, a warning will be produced telling users to specify ``--do-not-plot-allele-fraction`` to suppress this warning.
+* :issue:`78`: Fix bug in :command:`compute-copy-number` command where it threw an error "Different sample sets found" when the sample name consists of only numbers.
+
 0.19.0 (2022-09-13)
 -------------------
 

README.rst

@@ -20,9 +20,6 @@ README
 .. image:: https://anaconda.org/bioconda/pypgx/badges/downloads.svg
    :target: https://anaconda.org/bioconda/pypgx/files
 
-.. image:: https://anaconda.org/bioconda/pypgx/badges/installer/conda.svg
-   :target: https://conda.anaconda.org/bioconda
-
 Introduction
 ============
 

docs/cli.rst

@@ -940,15 +940,15 @@ run-ngs-pipeline
      CYP2D6 \
      CYP2D6-pipeline \
      --variants variants.vcf.gz \
-     --depth-of-coverage depth-of-coverage.tsv \
+     --depth-of-coverage depth-of-coverage.zip \
      --control-statistics control-statistics-VDR.zip
    
    [Example] To genotype the CYP2D6 gene from targeted sequencing data:
      $ pypgx run-ngs-pipeline \
      CYP2D6 \
      CYP2D6-pipeline \
      --variants variants.vcf.gz \
-     --depth-of-coverage depth-of-coverage.tsv \
+     --depth-of-coverage depth-of-coverage.zip \
      --control-statistics control-statistics-VDR.zip \
      --platform Targeted
 

docs/create.py

@@ -47,9 +47,6 @@
 .. image:: https://anaconda.org/bioconda/pypgx/badges/downloads.svg
    :target: https://anaconda.org/bioconda/pypgx/files
 
-.. image:: https://anaconda.org/bioconda/pypgx/badges/installer/conda.svg
-   :target: https://conda.anaconda.org/bioconda
-
 Introduction
 ============
 

pypgx/api/pipeline.py

@@ -248,10 +248,19 @@ def run_ngs_pipeline(
         alleles.to_file(f'{output}/alleles.zip')
 
         if not do_not_plot_allele_fraction:
-            os.mkdir(f'{output}/allele-fraction-profile')
-            plot.plot_vcf_allele_fraction(
-                imported_variants, path=f'{output}/allele-fraction-profile'
-            )
+            if imported_variants.data.empty:
+                message = (
+                    "Cannot plot allele fraction because input VCF is empty. "
+                    "Use '--do-not-plot-allele-fraction' to suppress this "
+                    "warning."
+                )
+                warnings.warn(message)
+            else:
+                os.mkdir(f'{output}/allele-fraction-profile')
+                plot.plot_vcf_allele_fraction(
+                    imported_variants,
+                    path=f'{output}/allele-fraction-profile'
+                )
 
     if large_var and depth_of_coverage is not None:
         if isinstance(depth_of_coverage, str):

pypgx/cli/run_ngs_pipeline.py

@@ -25,15 +25,15 @@
   CYP2D6 \\
   CYP2D6-pipeline \\
   --variants variants.vcf.gz \\
-  --depth-of-coverage depth-of-coverage.tsv \\
+  --depth-of-coverage depth-of-coverage.zip \\
   --control-statistics control-statistics-VDR.zip
 
 [Example] To genotype the CYP2D6 gene from targeted sequencing data:
   $ pypgx {fuc.api.common._script_name()} \\
   CYP2D6 \\
   CYP2D6-pipeline \\
   --variants variants.vcf.gz \\
-  --depth-of-coverage depth-of-coverage.tsv \\
+  --depth-of-coverage depth-of-coverage.zip \\
   --control-statistics control-statistics-VDR.zip \\
   --platform Targeted
 """

pypgx/sdk/utils.py

@@ -118,6 +118,7 @@ def from_file(cls, fn):
         elif 'SampleTable' in metadata['SemanticType']:
             with zf.open(f'{parent}/data.tsv') as fh:
                 data = pd.read_table(fh, index_col=0)
+                data.index = data.index.astype(str)
         elif 'VcfFrame' in metadata['SemanticType']:
             with zf.open(f'{parent}/data.vcf') as fh:
                 data = pyvcf.VcfFrame.from_file(fh)

pypgx/version.py

@@ -1 +1 @@
-__version__ = '0.19.0'
+__version__ = '0.20.0'