simplevcf
Simple VCF parser/writer with pure python
Examples
Read VCF
with simplevcf.vcfopen('some.vcf.gz') as reader:
for record in reader:
# process a recordRead, manipulate and write
with simplevcf.vcfopen('some.vcf.gz') as reader, with open('output.vcf) as f:
writer = simplevcf.Writer(f, reader.headers,
reader.samples)
for record in reader:
# manipulate a record
writer.write_record(one)Access to INFO and CALL
with simplevcf.vcfopen(test_file) as reader:
for one in reader:
print(
one.INFO['AC'], one.CALL['ERP107576_NovaSeq_SAMEA104707359']['GT'][0])
