mtbparser 0.2.1

A module that parses different diagnostic variant data.

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.

Changelog

v0.2.1

Fixes broken long description parsing in the setup.py, when trying to use pip for installation.

v0.2

First official release with PyPI deployment.