pybwtool 1.0.0

Python wrapper for the bwtool library.

Python wrapper for the bwtool library.

How do I install this package?

As usual, just download it using pip:

pip install pybwtool

Tests Coverage

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

Getting started

At the time of writing, the package includes just two methods from bwtool. If you need more, you are more than welcome to open a pull request adding the new feature or opening a new issue with the request. In the second case I’ll work on it when I’ll get the time.

Extract

The extract method returns a pandas Dataframe with the data from the regions of a bed file extracted from the given bigwig.

from pybwtool import extract

df = extract("path/to/my/bed", "path/to/my/bigwig")

Extract mean

The extract_mean method, similarly to the extract methon, returns a pandas Dataframe with the mean of the data from the regions of a bed file extracted from the given bigwig.

from pybwtool import extract_mean

df = extract_mean("path/to/my/bed", "path/to/my/bigwig")

Common fixes for getting bwtool to work

• For when the installation of bwtool gets stuck

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