Python wrapper for the bwtool library.


License
MIT
Install
pip install pybwtool==1.0.8

Documentation

pybwtool

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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 pybwtool

Tests Coverage

Since some software handling coverages sometimes get slightly different results, here's three of them:

Coveralls Coverage SonarCloud Coverage Code Climate Coverate

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.