DESCRIPTION.rst

About this module

This Python module was designed to provide a simple parser for different diagnostic variant information data.

How to use the SnvParser class

Parsing a SNV file following the formats described above is fairly simple. Just create an SnvParser object with the path to the tsv-file and specify its type by providing the correct header (SSnvHeader, GSnvHeader, ...).

from mtbparser.snv_parser import SnvParser
from mtbparser.snv_utils import SSnvHeader

# Path to a valid SNV tsv file, as specified in
# the file format documentation.
somatic_snv_file = "/path/to/mySSnv.tsv"

# Create parser object for somatic SNVs
parser = SnvParser(somatic_snv_file, SSnvHeader)

# Iterate through parsed SNV items and get the gene name
for snv_item in parser.getSNVs():
    print(snv_item.get_snv_info(SSnvHeader.GENE.name))

Detailed documentation

A more detailed documentation can be found on Github.