Metadata-Version: 2.1
Name: pybwtool
Version: 1.0.8
Summary: Python wrapper for the bwtool library.
Home-page: https://github.com/LucaCappelletti94/pybwtool
Author: Luca Cappelletti
Author-email: cappelletti.luca94@gmail.com
License: MIT
Description: pybwtool
        =========================================================================================
        |travis| |sonar_quality| |sonar_maintainability| |codacy|
        |code_climate_maintainability| |pip| |downloads|
        
        Python wrapper for the `bwtool library <https://github.com/CRG-Barcelona/bwtool>`_.
        Please take a look to the `bwtool wiki <https://github.com/CRG-Barcelona/bwtool/wiki#installation>`_ 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 <https://github.com/CRG-Barcelona/bwtool/issues/65>`_
        - `For when the installation of libbeato (a required library) gets stuck <https://github.com/CRG-Barcelona/libbeato/issues/6>`_
        
        
        
        .. |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&amp;utm_medium=referral&amp;utm_content=LucaCappelletti94/pybwtool&amp;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
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Provides-Extra: test
