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Python wrapper for the bwtool library.

Project description

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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:

Coveralls Coverage SonarCloud Coverage Code Climate Coverate

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")

Extract max

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

from pybwtool import extract_max

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

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