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mchowdh200 / samplot-ml

MIT License
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Error with sample_del.py #3

Closed lsantuari closed 2 years ago

lsantuari commented 3 years ago

When I run:

bcftools view -i 'SVTYPE="DEL"' $VCF \
    | bcftools query -f '%CHROM\t%POS\t%INFO/END[\t%SAMPLE,%GT]\n' \ 
    | python sample_del.py > $OUT/del.sample.bed # from git repo

on the VCF file "_ALL.wgs.integrated_sv_map_v1GRCh38.20130502.svs.genotypes.vcf.gz" I get the following error:

Traceback (most recent call last):
  File "sample_del.py", line 52, in <module>
    GT=line[6]))
  File "sample_del.py", line 12, in __init__
    self.AB = float(AB) if AB != '.' else AB
ValueError: could not convert string to float: 'HG00097,0|0'
brentp commented 3 years ago

bump. this is shown in the README and there's also an error about dhffc which doesn't exist in the file shown in the README.

mchowdh200 commented 2 years ago

I'm closing this issue due to its age. Since this issue, I made a lot of changes to the samplot-ml workflow. Everything is now handled with a snakemake pipeline that ensures all steps are run correctly and with the required versions of software/libraries. In my opinion, things should be way simpler to run and you don't have to worry about what version of tensorflow, bcftools, etc. you're running with.