bedshift 1.1.1
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Description:
bedshift 1.1.1
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:
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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