https://github.com/lucacappelletti94/pybwtool

Python wrapper for the bwtool library.
https://github.com/lucacappelletti94/pybwtool

Last synced: 3 months ago
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Python wrapper for the bwtool library.

Host: GitHub
URL: https://github.com/lucacappelletti94/pybwtool
Owner: LucaCappelletti94
Created: 2019-10-25T06:33:47.000Z (over 5 years ago)
Default Branch: master
Last Pushed: 2021-07-16T13:55:34.000Z (almost 4 years ago)
Last Synced: 2025-03-08T21:32:41.026Z (3 months ago)
Language: Python
Size: 62.4 MB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.rst

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README

        pybwtool

=========================================================================================

|travis| |sonar_quality| |sonar_maintainability| |codacy|

|code_climate_maintainability| |pip| |downloads|

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:

.. code:: shell

    pip install pybwtool

Tests Coverage

----------------------------------------------

Since some software handling coverages sometimes get slightly

different results, here's three of them:

|coveralls| |sonar_coverage| |code_climate_coverage|

Extract

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The :code:`extract` method returns a tuple of pandas Dataframes

with the data from the regions of a bed file extracted from the given bigwig.

.. code:: python

    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.

.. code:: python

    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:

.. code:: python

    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 `_

.. |travis| image:: https://travis-ci.org/LucaCappelletti94/pybwtool.png

   :target: https://travis-ci.org/LucaCappelletti94/pybwtool

   :alt: Travis CI build

.. |sonar_quality| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=alert_status

    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool

    :alt: SonarCloud Quality

.. |sonar_maintainability| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=sqale_rating

    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool

    :alt: SonarCloud Maintainability

.. |sonar_coverage| image:: https://sonarcloud.io/api/project_badges/measure?project=LucaCappelletti94_pybwtool&metric=coverage

    :target: https://sonarcloud.io/dashboard/index/LucaCappelletti94_pybwtool

    :alt: SonarCloud Coverage

.. |coveralls| image:: https://coveralls.io/repos/github/LucaCappelletti94/pybwtool/badge.svg?branch=master

    :target: https://coveralls.io/github/LucaCappelletti94/pybwtool?branch=master

    :alt: Coveralls Coverage

.. |pip| image:: https://badge.fury.io/py/pybwtool.svg

    :target: https://badge.fury.io/py/pybwtool

    :alt: Pypi project

.. |downloads| image:: https://pepy.tech/badge/pybwtool

    :target: https://pepy.tech/badge/pybwtool

    :alt: Pypi total project downloads 

.. |codacy| image:: https://api.codacy.com/project/badge/Grade/6f79fce7cb144f509ed584af3f950ab8

    :target: https://www.codacy.com/manual/LucaCappelletti94/pybwtool?utm_source=github.com&utm_medium=referral&utm_content=LucaCappelletti94/pybwtool&utm_campaign=Badge_Grade

    :alt: Codacy Maintainability

.. |code_climate_maintainability| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/maintainability

    :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/maintainability

    :alt: Maintainability

.. |code_climate_coverage| image:: https://api.codeclimate.com/v1/badges/68b5e35660142727406a/test_coverage

    :target: https://codeclimate.com/github/LucaCappelletti94/pybwtool/test_coverage

    :alt: Code Climate Coverate

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