{ "info": { "author": "MSR", "author_email": "fastlmm@microsoft.com", "bugtrack_url": null, "classifiers": [], "description": "PySnpTools\r\n====================\r\n\r\nPySnpTools is a library for reading and manipulating genetic data.\r\n\r\nMain Features:\r\n\r\nsnpreader: Efficiently read genetic PLINK formats including \\*.bed/bim/fam files.\r\n Also, efficiently read parts of files and standardize data. \r\n\r\nutil: In one line, intersect and re-order IIDs from snpreader and other sources.\r\n Also, efficiently extract a submatrix from an ndarray. \r\n\r\nutil.IntRangeSet: Efficiently manipulate ranges of integers - for example, genetic position - with set operators including union, intersection, and set difference. \r\n\r\nutil.pheno: Read the PLINK pheno type file format. \r\n\r\nFind the PySnpTools documentation (including links to tutorial slides, notesbooks, and video):\r\nhttp://microsoftgenomics.github.io/PySnpTools/\r\n\r\n\r\nWe originally created it for FaST-LMM, a program for performing genome-wide association studies (GWAS) on large data sets.\r\nhttp://research.microsoft.com/en-us/um/redmond/projects/MicrosoftGenomics/Fastlmm/\r\n\r\n\r\n\r\nQuick install:\r\n====================\r\n\r\nIf you have pip installed, installation is as easy as:\r\n\r\n pip install pysnptools\r\n\r\n\r\nDetailed Package Install Instructions:\r\n========================================\r\n\r\npysnptools has the following dependencies:\r\n\r\npython 2.7\r\n\r\nPackages:\r\n\r\n* numpy\r\n* scipy\r\n* pandas\r\n* cython\r\n\r\n\r\n(1) Installation of dependent packages\r\n-----------------------------------------\r\n\r\nWe highly recommend using a python distribution such as \r\nAnaconda (https://store.continuum.io/cshop/anaconda/) \r\nor Enthought (https://www.enthought.com/products/epd/free/).\r\nBoth these distributions can be used on linux and Windows, are free \r\nfor non-commercial use, and optionally include an MKL-compiled distribution\r\nfor optimal speed. This is the easiest way to get all the required package\r\ndependencies.\r\n\r\n\r\n(2) Installing from source\r\n-----------------------------------------\r\n\r\nGo to the directory where you copied the source code for fastlmm.\r\n\r\nOn linux:\r\n\r\nAt the shell, type: \r\n\r\n sudo python setup.py install\r\n\r\n\r\nOn Windows:\r\n\r\nAt the OS command prompt, type \r\n\r\n python setup.py install\r\n\r\n\r\n\r\nFor developers (and also to run regression tests)\r\n=========================================================\r\n\r\nWhen working on the developer version, first add the src directory of the package to your PYTHONPATH \r\nenvironment variable.\r\n\r\nFor building C-extensions, first make sure all of the above dependencies are installed (including cython)\r\n\r\nTo build extension (from .\\src dir), type the following at the OS prompt:\r\n\r\n python setup.py build_ext --inplace\r\n\r\nNote, if this fails with a gcc permission denied error, then specifying the correct compiler will likely fix the problem, e.g.\r\n\r\n python setup.py build_ext --inplace --compiler=msvc\r\n\r\n\r\nDon't forget to set your PYTHONPATH to point to the directory above the one named pysnptools in\r\nthe pysnptools source code. For e.g. if pysnptools is in the [somedir] directory, then\r\nin the unix shell use:\r\n\r\n export PYTHONPATH=$PYTHONPATH:[somedir]\r\n\r\nOr in the Windows DOS terminal,\r\none can use: \r\n\r\n set PYTHONPATH=%PYTHONPATH%;[somedir]\r\n\r\n(or use the Windows GUI for env variables).\r\n\r\nNote for Windows: You must have Visual Studio installed. If you have VisualStudio2008 installed \r\n(which was used to build python2.7) you need to nothing more. 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