Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. It is primarily built to integrate with software from Clinical Genomics, UPD Tool and rhocall, but is stand-alone.
Chromograph viewing is integrated a js module in Scout Chromograph can be used to visualise chromosomes in Scout (Screenshot from Scout with Chromograph):
Chromograph as used from the command line.
usage: chromograph [-h] [-a FILE] [-c FILE] [-f FILE] [-i FILE] [-m FILE]
[-r FILE] [-s FILE] [--step STEP] [--version] [-d FILE]
[-e] [-k FILE] [-n] [-u CHUNK] [-x] [--small] [--medium]
[--large]
optional arguments:
-h, --help show this help message and exit
-a FILE, --autozyg FILE
Plot regions of autozygosity from bed file [OPERATION]
-c FILE, --coverage FILE
Plot coverage from fixed step wig file [OPERATION]
-f FILE, --fracsnp FILE
Plot fraction of homozygous SNPs from wig file
[OPERATION]
-i FILE, --ideogram FILE
Plot ideograms from bed-file on format ['chrom',
'start', 'end', 'name', 'gStain'] [OPERATION]
-m FILE, --exom FILE Plot exom coverage from bed file [OPERATION]
-r FILE, --regions FILE
Plot UPD regions from bed file [OPERATION]
-s FILE, --sites FILE
Plot UPD sites from bed file [OPERATION]
--step STEP fixed step size (default 5000)
--version Display program version (1.3.0) and exit.
-d FILE, --outd FILE output dir
-e, --euploid Always output an euploid amount of files -even if some
are empty
-k FILE, --rgb FILE Set color (RGB hex, only with --coverage option)
-n, --norm Normalize data (wig/coverage)
-u CHUNK, --chunk CHUNK
Set Matplotlib.agg.path.chunksize (default 10000)
-x, --combine Write all graphs to one file (default one plot per
file)
--small
--medium
--large
One OPERATION Command is needed for Chromograph to produce output
$ ./chromograph.py --autozyg rhocall.bed --outd tmp/
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")
UPD bed files are supported on format:
'chrom', 'start', 'end', 'updType'
UPD bed files are generated with the tool UPDtool. An example call: TODO
Ideogram bed files are supported on format:
IDEOGRAM_FORMAT = ['chrom', 'start', 'end', 'name', 'gStain']
ROH wig files are supported on format:
['chrom', 'coverage', 'pos']
These can be created using Tiddit. For example: TODO
Chromograph runs in Python 3.
Package requirements:
- MatPlotLib
- Numpy
- Pandas
- Pyaml
pip install -r requirements.txt -e .
- Configuration file removed in version 0.3.2.