Chromograph

What is Chromograph?

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:

Usage, command line

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

Example

$ ./chromograph.py -r roh.wig --combine --step 3000

Usage, lib

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

Configuration file is config_chromograph.yml.

• chromosome_str used by roh and ideogram.
• chromosome_int used by upd.
• wig_step fixed size step in wig-files.

Data Formats

UPD BED

UPD bed files are supported on format:

'chrom', 'start', 'end', 'updType'

Ideogram BED

Ideogram bed files are supported on format:

IDEOGRAM_FORMAT = ['chrom', 'start', 'end', 'name', 'gStain']

ROH Coverage WIG

ROH wig files are supported on format:

['chrom', 'coverage', 'pos']

Requirements

Chromograph runs in Python 3.

Package requirements:

• MatPlotLib
• Numpy
• Pandas
• Pyaml

Installation

pip install numpy; pip install matplotlib; pip install pandas
pip install -e .