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A module that parses different diagnostic variant data.

Project Description

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.

Release History

This version
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0.2.7

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0.2.6

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0.2.5

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0.2.4

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0.2.3

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0.2.1

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0.2

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Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
mtbparser-0.2.7.tar.gz
(7.5 kB) Copy SHA256 Hash SHA256
Source None Feb 13, 2018

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