Metadata-Version: 2.1
Name: pysnptools
Version: 0.5.7
Summary: PySnpTools
Home-page: https://fastlmm.github.io/
Author: FaST-LMM Team
Author-email: fastlmm-dev@python.org
License: Apache 2.0
Project-URL: Bug Tracker, https://github.com/fastlmm/PySnpTools/issues
Project-URL: Documentation, http://fastlmm.github.io/PySnpTools
Project-URL: Source Code, https://github.com/fastlmm/PySnpTools
Keywords: gwas bioinformatics sets intervals ranges regions plink genomics file-format reader genotype bed-format writer python snps
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
License-File: LICENSE.md
License-File: AUTHORS.txt

PySnpTools
====================

PySnpTools is a library for reading and manipulating genetic data.

Main Features:

* [SnpReader](http://fastlmm.github.io/PySnpTools): 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](https://fastlmm.github.io/PySnpTools/#module-pysnptools.distreader): Efficiently work with
         unphased BGEN format and other diploid, biallelic distribution data.
          Also, efficiently read parts of files. See [Distribution IPython Notebook](https://nbviewer.jupyter.org/github/fastlmm/PySnpTools/blob/master/doc/ipynb/Dist.ipynb).

* [util](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util): In one line, intersect and re-order IIDs from snpreader and other sources.
          Also, efficiently extract a submatrix from an ndarray.

* [IntRangeSet](https://fastlmm.github.io/PySnpTools/#util-intrangeset): Efficiently manipulate ranges of integers - for example, genetic position - with set operators including union, intersection, and set difference.

* [mapreduce1](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util.mapreduce1): Run loops locally, on multiple processors, or on any cluster.

* [filecache](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util.filecache):  Read and write files locally or from/to any remote storage.

Install
-------

    pip install pysnptools

Documentation
-------------

* [Main Documentation](http://fastlmm.github.io/PySnpTools/) with examples. It includes links to tutorial slides, notebooks, and video.
* [Project Home and Full Annotated Bibliography](https://fastlmm.github.io/)

Code
----

* [PyPi](https://pypi.org/project/pysnptools/)
* [GitHub](https://github.com/fastlmm/PySnpTools)

Contacts
--------

* Email the developers at fastlmm-dev@python.org.
* [Join](mailto:fastlmm-user-join@python.org?subject=Subscribe) the user discussion and announcement list (or use [web sign up](https://mail.python.org/mailman3/lists/fastlmm-user.python.org)).
* [Open an issue](https://github.com/fastlmm/PySnpTools/issues) on GitHub.
