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BED file perturbations

Project description


Install with: pip install --user .

Command line

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

See: bedshift --help for parameters.


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')


test changes:

pip install --user .


if the tests complete, then bedshift is working properly

Project details

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