Which genome build again?

A species-agnostic tool to figure out the probable genome build of a file. Currently supports bigWig and bed files, and an easy method to add your own genome build.

Install with pip

pip install wgba

Usage:

Auto detect file extension

wgba your_file.bed

Use a specific file extension, if your extension is non-standard for example

wgba -f bed your_file.bed
wgba -f bigwig your_file.bigWig

You can use shell globs to match multiple files, all of which will be processed independently

wgba *.bed 

You can mix and match supported files

wgba a_bed_file.bed and_a_bigwig.bw and_another.bigWig

Check if all of your files are on the same build with -c, --check

wgba -c *.bed *.bw 

Summarise non-conforming chromosomes with -s, --summary

wgba -s bad_file.bed

Adjust the tolerance for build assignment with -t, --tol. This is useful if you know that one chromosome will never match.

wgba -t 2 one_bad_chromosome.bed

Add a genome build to the database

wgba -f add_build your_build.chrom.sizes

Issues

This was written in about an hour for my own use. If you find something not working, please raise an issue.