vcfparser

Python parser for parsing the genomics and transcriptomics VCF data.

Installation and setup

1. Clone this repo

git clone https://github.com/everestial/vcfparser
cd vcfparser

Usage

from vcf_parser import VcfParser
# instantiate a vcf object by passing file name
filepath = 'input_test.vcf'
vcf_object = VcfParser(filepath)

Get MetaInfo about the vcf file

metainfo = vcf_object.parse_metadata()
print(f'Fileformat for given vcf is : {metainfo.fileformat}')
print(f'Filters for given vcf are : {metainfo.filters_}')
print(f' Contig lines are : {metainfo.contig}')
print(f' Dictionary of infos is : {metainfo.infos_}')
print(f' Sample names are : {metainfo.sample_names}')
print("Raw lines are:")
print(metainfo.raw_meta_data)

Get Records from vcf file

records = vcf_object.parse_records() # this creates a generator object

for record in records:
    # you can access methods and attributes of record object as
    chrom = record.CHROM
    pos = record.POS
    id = record.ID
    ref = record.REF
    alt = record.ALT
    qual = record.QUAL
    filter = record.FILTER