Python wrapper for the bwtool library.
How do I install this package?
As usual, just download it using pip:
pip install pybwtool
Since some software handling coverages sometimes get slightly different results, here’s three of them:
extract method returns a tuple of pandas Dataframes
with the data from the regions of a bed file extracted from the given bigwig.
from pybwtool import extract results = extract( bed_path="path/to/my/bed_file.bed", bigwig_path="path/to/my/bigwig_file.bigwig" )
You can also run the extraction directly to a file, a thing that can get handy when you have to run a very big bed file. You just need to specify a target file.
from pybwtool import extract extract( bed_path="path/to/my/bed_file.bed", bigwig_path="path/to/my/bigwig_file.bigwig", target="target.bed" )
It is also possible to directly export to a compressed file just by adding the gzip extension, as follows:
from pybwtool import extract extract( bed_path="path/to/my/bed_file.bed", bigwig_path="path/to/my/bigwig_file.bigwig", target="target.bed.gz" )
Common fixes for getting bwtool to work
Consider looking at the Travis-CI configuration. If it works there, it should also work for you.
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