Skip to main content

PySnpTools

Project description

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.

Install

pip install pysnptools

Documentation

Code

Contacts

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pysnptools-0.5.11.tar.gz (221.6 kB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page