Metadata-Version: 2.1
Name: bgen-reader
Version: 1.1.5
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](https://img.shields.io/travis/limix/bgen-reader-py.svg?style=flat-square&label=linux%20%2F%20macos%20build)](https://travis-ci.org/limix/bgen-reader-py) [![AppVeyor](https://img.shields.io/appveyor/ci/Horta/bgen-reader-py.svg?style=flat-square&label=windows%20build)](https://ci.appveyor.com/project/Horta/bgen-reader-py)
        
        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/)
        
        ```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
        
        ```bash
        pip install bgen-reader
        ```
        
        from the command-line.
        
        ## Usage
        
        It is as simple as
        
        ```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).
        
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
