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| ignore: | ||
| - "misc/*.py" |
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| #!/usr/bin/env python | ||
| """Helper script to convert the HelixMtDb format to VCF. | ||
| The resulting file will look like this:: | ||
| ##fileformat=VCFv4.2 | ||
| ##contig=<ID=chrM,length=16569> | ||
| ##FILTER=<ID=PASS,Description="Variant passes all filters"> | ||
| ##INFO=<ID=AN,Number=1,Type=Integer,Description="Overall allele number (number of samples with non-missing genotype)"> | ||
| ##INFO=<ID=AC_hom,Number=1,Type=Integer,Description="Allele counts called as homoplasmic"> | ||
| ##INFO=<ID=AC_het,Number=1,Type=Integer,Description="Alelle counts called as heteroplasmic"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO | ||
| chrM 5 . A C . PASS AN=196554;AC_hom=1;AC_het=0 | ||
| chrM 10 . T C . PASS AN=196554;AC_hom=7;AC_het=1 | ||
| chrM 11 . C T . PASS AN=196554;AC_hom=0;AC_het=1 | ||
| """ | ||
|
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||
| import csv | ||
| import json | ||
| import sys | ||
|
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| import vcfpy | ||
|
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| #: Number of individiduals in HelixMtDb | ||
| AN = 196_554 | ||
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| def build_writer(): | ||
| """Build ``vcfpy`` writer for writing out the VCF file.""" | ||
| header = vcfpy.Header(samples=vcfpy.SamplesInfos(sample_names=[])) | ||
| header.add_line(vcfpy.HeaderLine("fileformat", "VCFv4.2")) | ||
| header.add_contig_line({"ID": "chrM", "length": 16569}) | ||
| header.add_filter_line({"ID": "PASS", "Description": "Variant passes all filters"}) | ||
| header.add_info_line( | ||
| { | ||
| "ID": "AN", | ||
| "Number": 1, | ||
| "Type": "Integer", | ||
| "Description": "Overall allele number (number of samples with non-missing genotype)", | ||
| } | ||
| ) | ||
| header.add_info_line( | ||
| { | ||
| "ID": "AC_hom", | ||
| "Number": 1, | ||
| "Type": "Integer", | ||
| "Description": "Allele counts called as homoplasmic", | ||
| } | ||
| ) | ||
| header.add_info_line( | ||
| { | ||
| "ID": "AC_het", | ||
| "Number": 1, | ||
| "Type": "Integer", | ||
| "Description": "Alelle counts called as heteroplasmic", | ||
| } | ||
| ) | ||
| return vcfpy.Writer(sys.stdout, header) | ||
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| def main(): | ||
| writer = build_writer() | ||
| reader = csv.DictReader(sys.stdin, delimiter="\t") | ||
| for row in reader: | ||
| locus = row["locus"].split(":") | ||
| chrom, pos = locus[0], int(locus[1]) | ||
| alleles = json.loads(row["alleles"]) | ||
| ac_hom = int(row["counts_hom"]) | ||
| ac_het = int(row["counts_het"]) | ||
| writer.write_record( | ||
| vcfpy.Record( | ||
| CHROM=chrom, | ||
| POS=pos, | ||
| ID=[], | ||
| REF=alleles[0], | ||
| ALT=[vcfpy.Substitution(vcfpy.SNV, alleles[1])], | ||
| QUAL=None, | ||
| FILTER=["PASS"], | ||
| INFO={ | ||
| "AN": AN, | ||
| "AC_hom": ac_hom, | ||
| "AC_het": ac_het, | ||
| }, | ||
| FORMAT=None, | ||
| calls=None, | ||
| ) | ||
| ) | ||
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| if __name__ == "__main__": | ||
| sys.exit(main()) |
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