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        "author": "Ryan Raaum",
        "author_email": "code@raaum.org",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "oldowan.mitomotifs is a small, pure Python, bioinformatic utility to (1)\ntransform human mitochondral DNA sequence data into variant sites relative to\nthe revised Cambridge Reference Sequence (rCRS) and (2) transform variant sites\ndata into DNA sequence. Further information on the rCRS and variant site\nnomenclature for human mtDNA sequences is available at the MitoMotifs_ website. \n\nInstallation Instructions\n=========================\n\nThis package is pure Python and has no dependencies outside of the standard\nlibrary. The easist way to install is using ``easy_install`` from the\nsetuptools_ package.  This usually goes something like this::\n\n\t$ easy_install oldowan.mitomotifs\n\nor on a unix-like system, assuming you are installing to the main Python\n``site-packages`` directory as a non-privileged user, this::\n\n\t$ sudo easy_install oldowan.mitomotifs\n\nYou may also use the standard python distutils setup method. Download the\ncurrent source archive from the file list towards the bottom of this page,\nunarchive it, and install. On Mac OS X and many other unix-like systems, having\ndownloaded the archive and changed to the directory containing this archive in\nyour shell, this might go something like::\n\n\t$ tar xvzf oldowan.mitomotifs*\n\t$ cd oldowan.mitomotifs*\n\t$ python setup.py install\n\nQuick Start\n===========\n\nImport ``seq2sites`` and ``sites2seq`` from oldowan.mitomotifs::\n\n  >>> from oldowan.mitomotifs import seq2sites, sites2seq\n\nConvert sequence to sites::\n\n  >>> seq = \"\"\"TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAA\n  GTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCC\n  AGCCACCATGAATATTGTACAGTACCATAAATACTTGACCACCTGTAGT\n  ACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCA\n  AGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAG\n  CCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGT\n  ACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATC\n  CCTTCTCGTCCC\"\"\"\n  >>> seq2sites(seq)\n\nSequences must be contiguous! Separate runs of sequence, such as HVR1 and HVR2\nwithout the intervening sequence interval, must be analyzed separately.\n\nThere is also a cutoff on the number of ambigous sites (N) allowed in the\nsequence. By default, this is 10 - but this is an option that can be set::\n\n  >>> seq2sites(seq, ambig_cutoff=20)\n\nConvert a list of variable sites to sequence. The default sequence region that\nis returned is hypervariable region 1 (HVR1), which is positions 16024 to 16365\nof the rCRS (in biological one-based numbering)::\n\n  >>> sites2seq('16129A 16223T')\n\nPredefined sequence regions are:\n\n- HVR1: 16024-16365\n- HVR2: 73-340\n- HVR1to2: 16024-340\n- coding: 577-15992\n- all: 1-16559\n\nSo, to convert a list of HVR2 sites to sequence::\n\n  >>> sites2seq('73G', region='HVR2')\n\nSites may also be provided in a list::\n\n  >>> sites2seq(['16129A', '16223T', '73G'], region='HVR1to2')\n\nThe rCRS sequence will be returned given an empty string, empty list, or the\nstring 'rCRS'. All of the following are equivalent::\n\n  >>> sites2seq('')\n  >>> sites2seq([])\n  >>> sites2seq('rCRS')\n\nArbitrary positions may be selected by passing a list of sites to the\n``region`` option::\n\n  >>> sites2seq('', region=[1,2,3])\n\nThe Python range function is convenient for this, but you must remember that\nthe range does not include it's ending position::\n\n  >>> sites2seq('', region=range(73,341))  # include 340, but not 341\n    \nRelease History ===============\n\n1.0.0 (August 16, 2008)\n    initial release of module.\n\n1.0.1 (August 22, 2008)\n    new 'add16k' option to sites2seq for abbreviated HVR1 sites (i.e. 16129A as 129A)\n\n\n.. _MitoMotifs: http://mitomotifs.raaum.org\n.. _setuptools: http://peak.telecommunity.com/DevCenter/EasyInstall",
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        "home_page": "http://mitomotifs.raaum.org",
        "keywords": "bioinformatics",
        "license": "MIT",
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        "name": "oldowan.mitomotifs",
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        "summary": "Transform human mtDNA sequence to variant sites and vice versa.",
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