Plotting allele fraction with empty VCF raises error

[sbslee]

A user reported a potential bug in the run-ngs-pipeline command where if the user provides an empty VCF, the command will throw an error complaining the VCF is empty when it should handle this type of situations.

I haven't had a chance to reproduce the issue yet, but it's possible and likely due to

pypgx/pypgx/api/plot.py

Line 348 in de490dd

def plot_vcf_allele_fraction(

[sbslee]

I was able to reproduce this error using a test VCF file (I removed all variants from chr22):

(fuc) sbslee@Seung-beens-MacBook-Air test % pypgx run-ngs-pipeline \       
CYP2D6 \
grch37-CYP2D6-pipeline \
--variants grch37-variants.vcf.gz
Saved VcfFrame[Imported] to: grch37-CYP2D6-pipeline/imported-variants.zip
Saved VcfFrame[Phased] to: grch37-CYP2D6-pipeline/phased-variants.zip
Saved VcfFrame[Consolidated] to: grch37-CYP2D6-pipeline/consolidated-variants.zip
Saved SampleTable[Alleles] to: grch37-CYP2D6-pipeline/alleles.zip
Traceback (most recent call last):
  File "/Users/sbslee/opt/anaconda3/envs/fuc/bin/pypgx", line 33, in <module>
    sys.exit(load_entry_point('pypgx', 'console_scripts', 'pypgx')())
  File "/Users/sbslee/Desktop/pypgx/pypgx/__main__.py", line 33, in main
    commands[args.command].main(args)
  File "/Users/sbslee/Desktop/pypgx/pypgx/cli/run_ngs_pipeline.py", line 159, in main
    pipeline.run_ngs_pipeline(
  File "/Users/sbslee/Desktop/pypgx/pypgx/api/pipeline.py", line 252, in run_ngs_pipeline
    plot.plot_vcf_allele_fraction(
  File "/Users/sbslee/Desktop/pypgx/pypgx/api/plot.py", line 396, in plot_vcf_allele_fraction
    ax1, ax2 = _plot_vcf_allele_fraction_one(
  File "/Users/sbslee/Desktop/pypgx/pypgx/api/plot.py", line 77, in _plot_vcf_allele_fraction_one
    imported_variants.data.plot_region(sample, ax=ax2, k='#AD_FRAC_REF', label='REF')
  File "/Users/sbslee/Desktop/fuc/fuc/api/pyvcf.py", line 3203, in plot_region
    raise ValueError('VcfFrame is empty')
ValueError: VcfFrame is empty

[sbslee]

This error could be avoided by using the --do-not-plot-allele-fraction option, but a more permanent solution is on its way.

[sbslee]

This issue has been fixed in the 0.20.0-dev branch. Basically, starting with 0.20.0 if the input VCF is empty the pipeline will not attempt to plot allele fraction and instead will produce a warning. The pipeline will also notify the user how to suppress the warning:

(fuc) sbslee@Seung-beens-MacBook-Air test % pypgx run-ngs-pipeline \
CYP2D6 \
grch37-CYP2D6-pipeline \
--variants grch37-variants.vcf.gz --force
Saved VcfFrame[Imported] to: grch37-CYP2D6-pipeline/imported-variants.zip
Saved VcfFrame[Phased] to: grch37-CYP2D6-pipeline/phased-variants.zip
Saved VcfFrame[Consolidated] to: grch37-CYP2D6-pipeline/consolidated-variants.zip
Saved SampleTable[Alleles] to: grch37-CYP2D6-pipeline/alleles.zip
/Users/sbslee/Desktop/pypgx/pypgx/api/pipeline.py:257: UserWarning: Cannot plot allele fraction because input VCF is empty. Use '--do-not-plot-allele-fraction' to suppress this warning.
  warnings.warn(message)
/Users/sbslee/Desktop/pypgx/pypgx/api/genotype.py:665: UserWarning: The user did not provide CNV calls even though the target gene is known to have SV. PyPGx will assume all of the samples do not have SV.
  warnings.warn(message)
Saved SampleTable[Genotypes] to: grch37-CYP2D6-pipeline/genotypes.zip
Saved SampleTable[Phenotypes] to: grch37-CYP2D6-pipeline/phenotypes.zip
Saved SampleTable[Results] to: grch37-CYP2D6-pipeline/results.zip