Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. It is primarily build to integrate with software form Clinical Genomics and UPD Tool but is stand-alone.
Integrated with Scout Chromograph can be used to visualise chromosomes:
Chromograph as used from the command line.
Usage: chromograph [COMMAND] [OPTIONS]
Command (one must be provided):
--upd <BED-filepath>
--ideo <BED-filepath>
--roh <WIG-filepath>
Options:
--help Show help message
--combine Default one image/png
--normalize normalize to mean (roh file only)
--step <int> Default 5000 (roh file only)
--outd <path> Default outdir is infile
$ ./chromograph.py -r roh.wig --combine --step 3000
Chromograph used as module. File must be provided, other arguments are optional. Example:
>>> import chromograph as chrm
>>> chrm.plot_ideogram("path_file.bed", 'combine', outdir=<path_output>)
>>> chrm.plot_upd(<file>, outd=<path>)
>>> chrm.plot_roh(<file>, 'combine', 'normalize', outd=<path>, step=<int>)
>>> chrm.plot_ideogram(file, 'combine', outd=<path>)
>>> chr.plot_ideogram("~/Work/files_test/cytoband.bed", 'combine', outd="/Users/Mikael/Downloads")
Configuration file is config_chromograph.yml.
chromosome_strused by roh and ideogram.chromosome_intused by upd.wig_stepfixed size step in wig-files.
UPD bed files are supported on format:
'chrom', 'start', 'end', 'updType'
Ideogram bed files are supported on format:
IDEOGRAM_FORMAT = ['chrom', 'start', 'end', 'name', 'gStain']
ROH wig files are supported on format:
['chrom', 'coverage', 'pos']
Chromograph runs in Python 3.
Package requirements:
- MatPlotLib
- Numpy
- Pandas
- Pyaml
pip install numpy; pip install matplotlib; pip install pandas
pip install -e .