A port of BCFtools's "plot-vcfstats"
This is basically a Python port of the plot-vcfstats utility included in
BCFtools. It's used to visualize the output of wthe bcftools stats command.
The original utility is a Perl script that wrote out a Python script to generate the figures with Matplotlib and then a LaTeX document
to combine them all in a PDF.
Currently the script vcf_stats_tools.py is as close of a copy to the Perl original as I can get, including writing
out a separate Python file and a LaTeX file.
It isn't pretty, that's for sure. Right now it's pretty Perl-ish and not idiomatic Python at all. It's been tested on several different types of VCFs, but is still experimental.
I'm hoping to turn this into a whole host of tools to work with VCF stats generated by bcftools stats. That will
include plotting, but also other analyses of the output. I might even try creating a pure-Python version of
bcftools stats so that it can be run on any platform (BCFtools doesn't work on Windows very well).
Here's some of the improvements I have in mind:
- Make everything more Pythonic (especially fixing up the data structures)
- Include all the Python code in one file so it doesn't have to write out a second file
- Use ReportLab to make the PDF
- Add option for a formatted HTML report