Parser of Igblast results into a csv file
Project description
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
-
pip install igblast-parser
-
conda install -c bioconda igblast-parser
-
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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for igblast_parser-0.0.4-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 09c7d445c283a4e94177ff7ca7de885faca5ba79288d1bd35bb6be45d38a8109 |
|
MD5 | 32051241bbab658f9e330cf134c14cd5 |
|
BLAKE2b-256 | a297a7519b78b44032dd784d839e82b63ee6d7880df0707e5e81a8ee4619b0b3 |