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)
* [Change Log](CHANGELOG.md)
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.
Raw data
{
"_id": null,
"home_page": "https://fastlmm.github.io/",
"name": "pysnptools",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "gwas bioinformatics sets intervals ranges regions plink genomics file-format reader genotype bed-format writer python snps",
"author": "FaST-LMM Team",
"author_email": "fastlmm-dev@python.org",
"download_url": "https://files.pythonhosted.org/packages/55/6f/22d291f5341fe3c7f7cc2412a1dbc179fb79d383806af5fd37e051d90191/pysnptools-0.5.11.tar.gz",
"platform": null,
"description": "PySnpTools\n====================\n\nPySnpTools is a library for reading and manipulating genetic data.\n\nMain Features:\n\n* [SnpReader](http://fastlmm.github.io/PySnpTools): Efficiently read genetic PLINK formats including \\*.bed/bim/fam files.\n Also, efficiently read parts of files, read kernel data, and standardize data.\n New features include multi-threaded BED reading, cluster-ready BED data, on-the-fly SNP generation,\n and larger in-memory data.\n\n* [DistReader](https://fastlmm.github.io/PySnpTools/#module-pysnptools.distreader): Efficiently work with\n unphased BGEN format and other diploid, biallelic distribution data.\n Also, efficiently read parts of files. See [Distribution IPython Notebook](https://nbviewer.jupyter.org/github/fastlmm/PySnpTools/blob/master/doc/ipynb/Dist.ipynb).\n\n* [util](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util): In one line, intersect and re-order IIDs from snpreader and other sources.\n Also, efficiently extract a submatrix from an ndarray.\n\n* [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.\n\n* [mapreduce1](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util.mapreduce1): Run loops locally, on multiple processors, or on any cluster.\n\n* [filecache](https://fastlmm.github.io/PySnpTools/#module-pysnptools.util.filecache): Read and write files locally or from/to any remote storage.\n\nInstall\n-------\n\n pip install pysnptools\n\nDocumentation\n-------------\n\n* [Main Documentation](http://fastlmm.github.io/PySnpTools/) with examples. It includes links to tutorial slides, notebooks, and video.\n* [Project Home and Full Annotated Bibliography](https://fastlmm.github.io/)\n\nCode\n----\n\n* [PyPi](https://pypi.org/project/pysnptools/)\n* [GitHub](https://github.com/fastlmm/PySnpTools)\n* [Change Log](CHANGELOG.md)\n\nContacts\n--------\n\n* Email the developers at <fastlmm-dev@python.org>.\n* [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)).\n* [Open an issue](https://github.com/fastlmm/PySnpTools/issues) on GitHub.\n",
"bugtrack_url": null,
"license": "Apache 2.0",
"summary": "PySnpTools",
"version": "0.5.11",
"project_urls": {
"Bug Tracker": "https://github.com/fastlmm/PySnpTools/issues",
"Documentation": "http://fastlmm.github.io/PySnpTools",
"Homepage": "https://fastlmm.github.io/",
"Source Code": "https://github.com/fastlmm/PySnpTools"
},
"split_keywords": [
"gwas",
"bioinformatics",
"sets",
"intervals",
"ranges",
"regions",
"plink",
"genomics",
"file-format",
"reader",
"genotype",
"bed-format",
"writer",
"python",
"snps"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "556f22d291f5341fe3c7f7cc2412a1dbc179fb79d383806af5fd37e051d90191",
"md5": "5a6517a18d7171d0633c441638470de7",
"sha256": "3643f8a58b65a77a9b536450b13f8d6908d0854aaf03fb0124b1cf2d414fc774"
},
"downloads": -1,
"filename": "pysnptools-0.5.11.tar.gz",
"has_sig": false,
"md5_digest": "5a6517a18d7171d0633c441638470de7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 221642,
"upload_time": "2023-11-12T22:45:15",
"upload_time_iso_8601": "2023-11-12T22:45:15.117635Z",
"url": "https://files.pythonhosted.org/packages/55/6f/22d291f5341fe3c7f7cc2412a1dbc179fb79d383806af5fd37e051d90191/pysnptools-0.5.11.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-12 22:45:15",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "fastlmm",
"github_project": "PySnpTools",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "pysnptools"
}