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    "info": {
        "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"
        ],
        "description": "oldowan.mitomotifs-cmdline provides the ``seq2sites`` and ``sites2seq`` command\nline scripts to covert human mitochondrial DNA sequences to lists of variant\nsites relative to the revised Cambridge Reference Seqeunce and vice versa.\nFurther information on the rCRS and variant site nomenclature for human mtDNA\nsequences is available at the MitoMotifs_ website. \n\nThis package is only the command line extension of the core oldwan.mitomotifs\nmodule. If you want just the Python libraries and not the command line tools,\nyou should go directly to that package.\n\nInstallation Instructions\n=========================\n\nThis package is pure Python and has only pure Python dependencies\n(oldowan.mitomotifs and oldowan.fasta) outside of the standard library. All of\nthese dependencies will be automatically installed if you use the setuptools_\n``easy_install`` tool.  This usually goes something like this::\n\n\t$ easy_install oldowan.mitomotifs-cmdline\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-cmdline\n\nYou may also use the standard python distutils setup method. You will have to\ndownload ind install oldowan.fasta and oldowan.mitomotifs first. Then, download\nthe current 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-cmdline*\n\t$ cd oldowan.mitomotifs-cmdline*\n\t$ python setup.py install\n\nQuick Start\n===========\n\nConvert sequences to sites::\n\n  $ seq2sites sequences.fasta\n\nConvert sequences to sites, saving the output to a file::\n\n  $ seq2sites sequences.fasta > sites.txt\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 --ambig-cutoff=20 sequences.fasta\n\nConvert a list of variable sites to sequence. The input file should be a\ncomma-seprated-values list with one entry per line, with name, N, and sites.\nSites should be separated by whitespace::\n\n  $ cat hvr1_sites.txt\n  Seq1,1,16129A\n  Seq2,1,16129A 16223T\n  Seq3,2,16223T\n  $ sites2seq hvr1_sites.txt\n\nThe default range of sequence returned is HVR1, defined as positions 16023 to\n16365 on the rCRS. All predefined ranges 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 --region=hvr2 hvr2_sites.txt\n\nAn arbitrary range may be selected. If the stop value is smaller than the\nstart, it is assumed that the range runs through the origin::\n\n  $ sites2seq --begin=16024 --end=340 dloop_sites.txt\n\nThe rCRS sequence will can be selected with 'rCRS' as the sites value::\n\n  $ cat sites.txt\n  Seq1,1,rCRS\n  Seq2,1,16129A 16223T\n\nRelease History ===============\n\n1.0.0 (August 16, 2008)\n    initial release of module.\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",
        "maintainer": null,
        "maintainer_email": null,
        "name": "oldowan.mitomotifs-cmdline",
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