You can get genome_coverage_plotter by pulling it from git:
git clone https://github.com/matted/genome_coverage_plotter.git
To run genome_coverage_plotter, several Python packages are required. On a Ubuntu-like
system, these commands will get the appropriate dependencies:
sudo apt-get install python python-dev build-essential python-setuptools python-numpy python-scipy python-pylab python-pandas sudo easy_install pysam seaborn
If you want the genome_coverage_plotter tools on your system path (and want to get the
dependencies automatically), install it with:
sudo python setup.py install
There is also a Docker image that has genome_coverage_plotter and its dependencies
Run the script on a sorted, indexed bam file:
python plot_coverage.py yeast_test_small.bam
The output is:
chromosome normalized_coverage chr10 1.0000 chr11 1.0264 chr12 1.0556 chr13 1.0000 chr14 1.0000 chr15 0.9444 chr16 1.0000 chr1 0.8889 chr2 1.0000 chr3 1.0556 chr4 1.0083 chr5 1.0000 chr6 1.0472 chr7 1.0000 chr8 1.0889 chr9 0.8889
And it creates an output plot image based on the input filename, like:
The chromosomes are ordered based on their order in the input file.
All the parameters and plot options are currently hardcoded.