vcf_validator

This python package parses the vcf file and checks the VCF attributes with respect to the paper: https://f1000research.com/articles/11-231

Installing the package:

pip install vcfvalidator

How to use parser:

First import the package using following command:

from vcf_validator import vcf_parser

Create and object of the class:

parser = vcf_parser.vcf_parser()

Then call the method:

parser.parse_as_chunks("m", 1000, True)

The method parse_as_chunks parses the file and check for VCF header attributes for now.

Parameters for method:

1. data to be parsed: for metadata use "m" and for header data use "h"

2. Chunk size.

3. "True" to stop the file after parsing header data, "False" to continue the parser till the end of the file.

Responisble person

For further details please contact: Dr. Matthias Lange (lange@ipk-gatersleben.de)

Location of files

The parser generates the output in log files, which could be found in the directory where the scripts is located.