Metadata-Version: 2.1
Name: bgen_reader
Version: 1.1.0
Summary: Bgen file format reader
Home-page: https://github.com/limix/bgen-reader-py
Author: Danilo Horta
Author-email: horta@ebi.ac.uk
Maintainer: Danilo Horta
Maintainer-email: horta@ebi.ac.uk
License: MIT
Download-URL: https://github.com/limix/bgen-reader-py
Description: bgen-reader
        ===========
        
        |Travis| |AppVeyor| |Gitter|
        
        A `BGEN file format <http://www.well.ox.ac.uk/~gav/bgen_format/>`__
        reader.
        
        BGEN is a file format for storing large genetic datasets. It supports
        both unphased genotypes and phased haplotype data with variable ploidy
        and number of alleles. It was designed to provides a compact data
        representation without sacrificing variant access performance.
        
        This Python package is a wrapper around the `bgen
        library <https://github.com/limix/bgen>`__, a low-memory footprint
        reader that efficiently reads BGEN files. It fully supports the BGEN
        format specifications: 1.2 and 1.3; as well as their optional compressed
        formats.
        
        Install
        -------
        
        It requires the bgen C library which can be installed via
        `conda <https://conda.io/docs/>`__
        
        .. code:: bash
        
            conda install -c conda-forge bgen
        
        Alternatively, the `bgen-reader
        repository <https://github.com/limix/bgen>`__ provides instructions for
        manual installation.
        
        Once bgen C library is installed, simply enter
        
        .. code:: bash
        
            pip install bgen-reader
        
        from the command-line.
        
        Usage
        -----
        
        It is as simple as
        
        .. code:: python
        
            # example.py file
            from bgen_reader import read_bgen
        
            bgen = read_bgen("example.bgen", verbose=False)
        
            print(bgen['variants'].head())
            print(bgen['samples'].head())
            print(len(bgen['genotype']))
            print(bgen['genotype'][0].compute())
        
        The output should something similar to
        
        ::
        
            chrom       id  nalleles   pos    rsid
            0    01  SNPID_2         2  2000  RSID_2
            1    01  SNPID_3         2  3000  RSID_3
            2    01  SNPID_4         2  4000  RSID_4
            3    01  SNPID_5         2  5000  RSID_5
            4    01  SNPID_6         2  6000  RSID_6
                     id
            0  sample_001
            1  sample_002
            2  sample_003
            3  sample_004
            4  sample_005
            199
            [[        nan         nan         nan]
            [ 0.02780236  0.00863674  0.9635609 ]
            [ 0.01736504  0.04968414  0.93295083]
            ...,
            [ 0.01419069  0.02810669  0.95770262]
            [ 0.91949463  0.05206298  0.02844239]
            [ 0.00244141  0.98410029  0.0134583 ]]
        
        Problems
        --------
        
        If you encounter any issue, please, `submit
        it <https://github.com/limix/bgen-reader-py/issues/new>`__.
        
        Authors
        -------
        
        -  `Danilo Horta <https://github.com/horta>`__
        
        License
        -------
        
        This project is licensed under the `MIT
        License <https://raw.githubusercontent.com/limix/bgen-reader-py/master/LICENSE.md>`__.
        
        .. |Travis| image:: https://img.shields.io/travis/limix/bgen-reader-py.svg?style=flat-square&label=linux%20%2F%20macos%20build
           :target: https://travis-ci.org/limix/bgen-reader-py
        .. |AppVeyor| image:: https://img.shields.io/appveyor/ci/Horta/bgen-reader-py.svg?style=flat-square&label=windows%20build
           :target: https://ci.appveyor.com/project/Horta/bgen-reader-py
        .. |Gitter| image:: https://img.shields.io/gitter/room/limix/bgen-reader-py.js.svg?style=flat-square
           :target: https://gitter.im/bgen-reader-py/Lobby
        
Keywords: bgen,reader,genetics
Platform: Windows
Platform: MacOS
Platform: Linux
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
