ARCHIVED REPOSITORY.

As of 2026, bedshift has been integrated into the geniml project. all functionality is now availalbe in that package.

you can now find more information at

https://github.com/databio/geniml

Bedshift

Docs: bedshift.databio.org

Install from PyPi: pip install bedshift

Install from local repository: pip install .

Command line

Run with:

bedshift -l tests/hg38.chrom.sizes -b tests/test.bed

See bedshift -h for parameters.

Python

import bedshift

bedshifter = bedshift.Bedshift('tests/test.bed', 'hg38.chrom.sizes')
bedshifter.all_perturbations(addrate=0.3, addmean=320.0, addstdev=20.0,
							 shiftrate=0.3, shiftmean=-10.0, shiftstdev=120.0,
							 cutrate=0.1,
							 mergerate=0.11,
							 droprate=0.03)
# can also run single operations: shift, add, cut, merge, drop

bedshifter.to_bed('test_output.bed')

Development

Run tests (from this directory):

python -m unittest

Double check the output files to see if the regions make sense.

build docs: