bedshift 1.0.0

BED file perturbations

Bedshift

Install with: pip install --user .

Command line

Run with: bedshift -b BEDFILE or ./bedshift.sh if running bedshift on multiple bedfiles with a set of parameters, which are editable in bedshift.sh.

See: bedshift --help for parameters.

Python

import bedshift

bedshifter = bedshift.Bedshift('tests/test.bed')
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

test changes:

pip install --user .

./run-tests.sh

if the tests complete, then bedshift is working properly