Metadata-Version: 2.1
Name: microplink
Version: 0.0.1
Summary: PLINK file processing with numba
Home-page: https://github.com/ammodramus/microplink
Author: Peter Wilton
Author-email: peterrwilton@gmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=2.7
Description-Content-Type: text/markdown
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: numba

`microplink`
===========

This class provides a minimal and fast interface for retrieving genotypes
from Plinks's BED/BIM/FAM file trios. The BED file must fit in memory.

Requirements
------------

`numpy`, `pandas`, and `numba`. These are included with many Python
distributions.

Installation
------------

Run `pip install microplink` or clone this repository and run `python setup.py
install` from the repository directory.

Usage
-----

Typical usage:

    import microplink as mic

    # Equivalent to `pf = mic.PlinkFiles('test.bed', 'test.bim', 'test.fam')`
    pf = mic.PlinkFiles('test')

    # fetch by chromosome and position
    pf.get_genotypes(chromosome=1, position=10000)

    # fetch by variant name (often RSID)
    pf.get_genotypes(snp='rs1235123')

    # fetch by SNP integer index
    pf.get_genotypes(snp_index=0)


