aerijman / igblast-parser

Simple parser of igblast results into a csv table

Simple parser of igblast results

Igblast allows to view the matches to the germline V, D and J genes, details at rearrangement junctions and a lot more (see documentation).

The output includes a lot of information in a format that can't be directly used in statistical analyses.

This simple script parses igblast output into a csv formatted table, easy to understand and ready to include in a statistical analysis.

Installation

1. pip install igblast-parser

2. conda install -c bioconda igblast-parser

3. python setup.py install

Usage

docs

While docs are not ready:

Command line executable in unix-like systems:

	cat <igblast.output> | igblast-parser

Pipe is not obligatory as the input could be specified with the argument --in

optional argument: --out to specify the prefix of the output csv file

	igblast-parser --in <igblast.output> --out <parser_output>

In interactive python or script

	f_in = open('igblast.output','r')

	# dictionary with UMI as primary key and multiple keys/UMI
	d = igblast_parse(f)

	# pandas provides very nice tables
 	import pandas
	df = pandas.DataFrame(d).T