Metadata-Version: 2.1
Name: cbgen
Version: 1.0.1
Summary: Python wrapper around bgen library
Home-page: https://github.com/limix/cbgen
Author: Danilo Horta
Author-email: horta@ebi.ac.uk
Maintainer: Danilo Horta
Maintainer-email: horta@ebi.ac.uk
License: MIT
Description: # cbgen
        
        Python wrapper around a BGEN library.
        ([cbgen documentation](https://cbgen.readthedocs.io)).
        
        [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) 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
        provide 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.
        
        ## Installation
        
        ```bash
        pip install cbgen
        ```
        
        ## Usage example
        
        ```python
        >>> import cbgen
        >>>
        >>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen"))
        >>> bgen.create_metafile("haplotypes.bgen.metafile")
        >>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile")
        >>> print(mf.npartitions)
        1
        >>> print(mf.nvariants)
        4
        >>> print(mf.partition_size)
        4
        >>> part = mf.read_partition(0)
        >>> gt = bgen.read_genotype(part.variants.offset[0])
        >>> print(gt.probability)
        [[1. 0. 1. 0.]
         [0. 1. 1. 0.]
         [1. 0. 0. 1.]
         [0. 1. 0. 1.]]
        >>> mf.close()
        >>> bgen.close()
        ```
        
        ## Authors
        
        * [Carl Kadie](https://github.com/CarlKCarlK)
        * [Danilo Horta](https://github.com/horta)
        
        ## License
        
        This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE).
        
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
