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BED file perturbations

Project description



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.


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,
# can also run single operations: shift, add, cut, merge, drop



Run tests (from this directory):

python -m unittest

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

build docs:

Project details

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