lnalinaf/vcf_adjunct_parser

Customized VCF parser

VCF Adjunct Parser

Small library for parsing vcf files. Based on vcf_parser

usage examples:

- Calculate the ploidy of presented individuals
- Calculate the histogram for distribution of lengths of intervals between heterozygotes

Installation

>git clone https://github.com/fkbyf14/vcf_adjunct_parser.git
>cd vcf_adjunct_parser
>python setup.py install

Usage

After get the file vcf_adjunct_parser/usages/test_task.py:

• output: the number of ploidy (1 for haploidy, 2 for diploidy and so on)

>python3 test_task.py --file test_vcf.vcf

• output: distribution of lengths of intervals between heterozygotes in dictionary: {distance: number of neighbouring heterozygotes}, matplotlib drawing; for perform task target output: array H - histogram of lengths distribution is necessary to uncomment code block after such the comm (# for perform task target output: array H - histogram of lengths distribution)

>python3 test_task.py --file test_vcf.vcf --individual father