pybwtool 1.0.8

Python wrapper for the bwtool library.

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:

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.

• For when the installation of bwtool gets stuck
• For when the installation of libbeato (a required library) gets stuck