Which genome build again?
Project description
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.
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