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        "author": "Carlos Pe\u00f1a",
        "author_email": "mycalesis@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: Implementation :: CPython",
            "Programming Language :: Python :: Implementation :: PyPy",
            "Topic :: Utilities"
        ],
        "description": "===============\nPrimer designer\n===============\n\n.. list-table::\n    :stub-columns: 1\n\n    * - tests\n      - | |travis| |requires| |coveralls|\n        | |quantified_code|\n    * - package\n      - |version| |wheel| |supported_versions| |supported_implementations|\n\n.. |travis| image:: https://travis-ci.org/carlosp420/primer-designer.svg?branch=master\n    :alt: Travis-CI Build Status\n    :target: https://travis-ci.org/carlosp420/primer-designer\n\n.. |requires| image:: https://requires.io/github/carlosp420/primer-designer/requirements.svg?branch=master\n    :alt: Requirements Status\n    :target: https://requires.io/github/carlosp420/primer-designer/requirements/?branch=master\n\n.. |coveralls| image:: https://coveralls.io/repos/carlosp420/primer-designer/badge.svg?branch=master&service=github\n    :alt: Coverage Status\n    :target: https://coveralls.io/r/carlosp420/primer-designer\n\n.. |version| image:: https://img.shields.io/pypi/v/primer_designer.svg?style=flat\n    :alt: PyPI Package latest release\n    :target: https://pypi.python.org/pypi/primer_designer\n\n.. |quantified_code| image:: https://www.quantifiedcode.com/api/v1/project/23f9326bf0484aebb952f2d821969436/badge.svg\n    :target: https://www.quantifiedcode.com/app/project/23f9326bf0484aebb952f2d821969436\n    :alt: Code issues\n\n.. |wheel| image:: https://img.shields.io/pypi/wheel/primer_designer.svg?style=flat\n    :alt: PyPI Wheel\n    :target: https://pypi.python.org/pypi/primer_designer\n\n.. |supported_versions| image:: https://img.shields.io/pypi/pyversions/primer_designer.svg?style=flat\n    :alt: Supported versions\n    :target: https://pypi.python.org/pypi/primer_designer\n\n.. |supported_implementations| image:: https://img.shields.io/pypi/implementation/primer_designer.svg?style=flat\n    :alt: Supported implementations\n    :target: https://pypi.python.org/pypi/primer_designer\n\nDesigns primers from a FASTA file using primers4clades website\n\n* Free software: BSD license\n\nInstallation\n============\n\n::\n\n    pip install primer_designer\n\nUsage\n=====\nIt will send a FASTA alignment to `primers4clades`_ in order to design\ndegenerate primers. Input data needed is an alignment in FASTA format\ncontaining at least 4 sequences.\nIt is recommended that the beginning of each FASTA sequence description\ncontains the taxon name between square brackets.\n\nParameters:\n\n* folder (str):         path of folder containing the FASTA file alignments\n* tm (str):             temperature\n* min_amplength (str):  minimum amplicon length\n* max_amplength (str):  maximum amplicon length\n* gencode (str):        genetic code. See below for all available genetic codes\n* clustype (str):       cluster distance metric: ``dna``, ``protein``.\n* amptype (str):        substitution model used to estimate phylogenetic information\n* email (str):          your email address so that primer4clades can send you email with detailed results\n\nExample:\n\n.. code-block:: python\n\n    >>> # The values shown are the default. Change them if needed.\n    >>> from primer_designer import PrimerDesigner\n    >>> pd = PrimerDesigner()\n    >>> pd.folder = \"alignments\"   # folder containing the FASTA file alignments\n    >>> pd.tm = \"55\"               # annealing temperature\n    >>> pd.min_amplength = \"250\"   # minimum amplicon length\n    >>> pd.max_amplength = \"500\"   # maximum amplicon length\n    >>> pd.gencode = \"universal\"   # see below for all available genetic codes\n    >>> pd.mode  = \"primers\"\n    >>> pd.clustype = \"dna\"\n    >>> pd.amptype = \"dna_GTRG\"    # substitution model used to estimate phylogenetic information\n    >>> pd.email = \"youremail@email.com\"   # primer4clades will send you an email with very detailed results\n    >>> pd.design_primers()\n\nThe best primer pairs will be printed to your screen. Detailed results will\nbe saved as HTML files in your alignments folder. But it is recommended if\nyou also get the results by email. primers4clades_ will send you one email\nfor each alignment.\nThe genetic code table (variable ``gencode``) can be any of the following:\n\n* ``universal`` for standard\n* ``2`` for vertebrate mitochondrial\n* ``3`` for yeast mitochondrial\n* ``4`` for mold and protozoa mitochondrial\n* ``5`` for invertebrate mitochondrial\n* ``6`` for ciliate\n* ``9`` for echinoderm and flatworm\n* ``10`` for  euplotid nuclear\n* ``11`` for  bacterial and plastid\n* ``12`` for  alternative yeast nuclear\n* ``13`` for  ascidian mitochondrial\n* ``14`` for  flatworm mitochondrial\n* ``15`` for  Blepharisma nuclear\n* ``16`` for  Chlorophycean mitochondrial\n* ``21`` for  Trematode mitochondrial\n* ``22`` for  Scenedesmus obliquus mitochondrial\n* ``23`` for  Thraustochytrium mitochondrial\n\nThe evolutionary substitution model can be any of the following (variable ``amptype``):\n\n* ``protein_WAGG``  for protein WAG+G\n* ``protein_JTTG``  for protein JTT+G\n* ``protein_Blosum62G``  for protein Blosum62+G\n* ``protein_VTG``  for protein VT+G\n* ``protein_DayhoffG``  for protein Dayhoff+G\n* ``protein_MtREVG``  for protein MtREV+G\n* ``dna_HKYG``  for dna HKY+G\n* ``dna_GTRG``  for dna GTR+G\n* ``dna_K80G``  for dna K80+G\n* ``dna_TrNG``  for dna TrN+G\n* ``dna_JC69G``  for dna JC69+G\n\n.. _primers4clades: http://floresta.eead.csic.es/primers4clades/#0\n\nDocumentation\n=============\n\nhttps://primer-designer.readthedocs.org/\n\nDevelopment\n===========\n\nTo run the all tests run::\n\n    tox\n\nRelease History\n---------------\n\n0.2.0 (2015-10-27)\n++++++++++++++++++\n\n- After all FASTA alignments are processed, a report will be produced with the\n  codehop, relaxed and degen primers for the best amplicon (higher quality and\n  longer expeced sequence).\n\n0.1.1 (2015-10-23)\n++++++++++++++++++\n\n- Fixed bug that caused infinite loop if input FASTA alignment was incorrect and\n  primer4clades could not generate primers for.\n\n0.1.0 (2015-10-22)\n++++++++++++++++++\n\n- Add taxon name to description of FASTA seqs if given by user.\n\n0.0.1 (2015-10-22)\n++++++++++++++++++\n\n- Some refactoring and testing.\n- Updated requirements.\n- Added test rule to Makefile.\n- Small fixes of style to code.\n- Replaced name of changelog to history.\n\n0.0.0 (2015-10-06)\n++++++++++++++++++\n\n- First release on PyPI.",
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