Python wrapper for the bwtool library.
Project description
Python wrapper for the bwtool library.
How do I install this package?
As usual, just download it using pip:
pip install pybwtoolTests 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")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")Common fixes for getting bwtool to work
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