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

Requires Python 3.11.5 or later. Python 3.15 qualification is in progress.

HDF5 support is optional. To read or write HDF5 files, install:

pip install pysnptools[hdf5]

Existing HDF5 users upgrading from an earlier release should install this extra.

If you need support for BGEN files, instead do:

pip install pysnptools[bgen]

Documentation

• Main Documentation with examples. It includes links to tutorial slides, notebooks, and video.
• Project Home and Full Annotated Bibliography

Code

• PyPi
• GitHub
• Change Log

Contacts

• Email the developers at fastlmm-dev@python.org.
• Join the user discussion and announcement list (or use web sign up).
• Open an issue on GitHub.