bedshift 0.2.0

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

from bedshift import bedshift

bedshifter = bedshift.Bedshift()

df = bedshifter.read_bed('test.bed')
df = bedshifter.all_perturbations(df, 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.write_bed(df, 'output_file.bed')

Development

test changes:

pip install --user .

./run-tests.sh

if the tests complete, then bedshift is working properly