PySnpTools
PySnpTools is a library for reading and manipulating genetic data.
Main Features:
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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.
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DistReader: Efficiently work with
unphased BGEN format and other diploid, biallelic distribution data.
Also, efficiently read parts of files. See Distribution IPython Notebook.
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util: In one line, intersect and re-order IIDs from snpreader and other sources.
Also, efficiently extract a submatrix from an ndarray.
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IntRangeSet: Efficiently manipulate ranges of integers - for example, genetic position - with set operators including union, intersection, and set difference.
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mapreduce1: Run loops locally, on multiple processors, or on any cluster.
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filecache: Read and write files locally or from/to any remote storage.
Install
pip install pysnptools
Documentation
Code
Contacts