pybwtool
Python wrapper for the bwtool library. Please take a look to the bwtool wiki for notes on the installation process and to the known issues listed below within this readme.
How do I install this package?
As usual, just download it using pip:
pip install pybwtoolTests Coverage
Since some software handling coverages sometimes get slightly different results, here's three of them:
Extract
The 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.
