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PySnpTools

PySnpTools is a library for reading and manipulating genetic data.

Main Features:

SnpReader: Efficiently read genetic PLINK formats including *.bed/bim/fam files. Also, efficiently read parts of files, read kernel data, and standardize data. New features include multi-threaded BED reading, cluster-ready BED data, on-the-fly SNP generation, and larger in-memory data.
DistReader: Efficiently work with unphased BGEN format and other diploid, biallelic distribution data. Also, efficiently read parts of files. See Distribution IPython Notebook.
util: In one line, intersect and re-order IIDs from snpreader and other sources. Also, efficiently extract a submatrix from an ndarray.
IntRangeSet: Efficiently manipulate ranges of integers - for example, genetic position - with set operators including union, intersection, and set difference.
mapreduce1: Run loops locally, on multiple processors, or on any cluster.
filecache: Read and write files locally or from/to any remote storage.

pip install pysnptools

If you need support for BGEN files, instead do:

pip install pysnptools[bgen]

Main Documentation with examples. It includes links to tutorial slides, notebooks, and video.
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