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    "info": {
        "author": "Lars Sch\u00f6ning",
        "author_email": "lays@biosustain.dtu.dk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Other Environment",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: Apache Software License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Gnomic\n======\n\n.. image:: https://travis-ci.org/biosustain/gnomic.svg?branch=master\n    :target: https://travis-ci.org/biosustain/gnomic\n\n.. image:: https://zenodo.org/badge/47830031.svg\n   :target: https://zenodo.org/badge/latestdoi/47830031\n\nGnomic is a human\u2013 and computer\u2013readable representation of microbial genotypes and phenotypes. The ``gnomic``\nPython package contains a parser for the Gnomic grammar able to interpret changes over multiple generations.\n\nThe first formal guidelines for microbial genetic nomenclature were drawn up in the 1960s. These traditional nomenclatures are too\nambiguous to be useful for modern computer-assisted genome engineering. The *gnomic* grammar is an improvement over existing nomenclatures, designed to be clear, unambiguous, computer\u2013readable and describe genotypes at various levels of detail.\n\nInstallation\n------------\n\n.. code-block:: bash\n\n    pip install gnomic\n\nLanguage grammar\n----------------\n\nThe grammar consists of a list of genotype or phenotype designations, separated by\nspaces and/or commas. The designations are described using the following nomenclature:\n\n============================================================= ==================================\nDesignation                                                   Grammar expression\n============================================================= ==================================\n``feature`` deleted                                           ``-feature``\n``feature`` at ``locus`` deleted                              ``-feature@locus``\n``feature`` inserted                                          ``+feature``\n``site`` replaced with ``feature``                            ``site>feature``\n``site`` (multiple integration) replaced with ``feature``     ``site>>feature``\n``site`` at ``locus`` replaced with ``feature``               ``site@locus>feature``\n``feature`` of ``organism``                                   ``organism/feature``\n``feature`` with ``type``                                     ``type.feature``\n``feature`` with variant                                      ``feature(variant)``\n``feature`` with list of variants                             ``feature(var1, var2)`` or ``feature(var1; var2)``\n``feature`` with accession number                             ``feature#GB:123456``\n``feature`` by accession number                               ``#GB:123456``\naccession number                                              ``#database:id`` or ``#id``\nfusion of ``feature1`` and ``feature2``                       ``feature1:feature2``\ninsertion of two fused features                               ``+feature1:feature2``\ninsertion of a list of features or fusions                    ``+{..insertables}``\nfusion of a list and a feature                                ``{..insertables}:feature``\na non-integrated plasmid                                      ``(plasmid)`` or ``(plasmid ...insertables)``\nintegrated plasmid vector with required insertion site        ``site>(vector ..insertables)``\n============================================================= ==================================\n\n\nFeature variants\n^^^^^^^^^^^^^^^^\n\nFeatures may have one or more variants, separated by colon \";\" or comma \",\".\n\nFor example: ``geneX(cold-resistant; heat-resistant)``\n\nVariants can either be identifiers (using the characters a-z, 0-9, \"-\" and \"_\") or be sequence variants following\nthe HGVS `Sequence Variant Nomenclature <http://www.hgvs.org/varnomen>`_.\n\nFor example: ``geneY(c.123G>T)``\n\n\nExample usage\n-------------\n\nIn this example, we parse `\"EcGeneA \u0394siteA::promoterB:EcGeneB \u0394geneC\"` and `\"\u0394geneA\"` in *gnomic* syntax:\n\n.. code-block:: python\n\n   >>> from gnomic import Genotype\n   >>> g1 = Genotype.parse('+Ec/geneA(variant) siteA>P.promoterB:Ec/geneB -geneC')\n   >>> g1.added_features\n   {Feature(organism='Ec', name='geneA', variant=('variant',)),\n    Feature(organism='Ec', name='geneB'),\n    Feature(type='P', name='promoterB')}\n   >>> g1.removed_features\n   {Feature(name='geneC'),\n    Feature(name='siteA')}\n\n   >>> g2 = Genotype.parse('-geneA', parent=g1)\n   >>> g2.added_features\n   {Feature(type='P', name='promoterB'),\n    Feature(name='geneB', organism='Ec')}\n   >>> g2.removed_features\n   {Feature(name='siteA'),\n    Feature(name='geneC')}\n    >>> g2.changes()\n    (Change(multiple=False,\n            after=Fusion(annotations=(Feature(type='P', name='promoterB'), Feature(organism='Ec', name='geneB'))),\n            before=Feature(name='siteA')),\n     Change(multiple=False, before=Feature(name='geneC')))\n\n    >>> g2.format()\n    '\u0394siteA\u2192P.promoterB:Ec/geneB \u0394geneC'\n\n\nDevelopment\n-----------\n\nTo rebuild the gnomic parser using `grako` (version 3.18.1), run:\n\n::\n\n    grako gnomic-grammar/genotype.enbf -o gnomic/grammar.py -m Gnomic\n    \nReferences\n-----------\n\n- `Wikipedia \u2014 Bacterial genetic nomenclature <http://en.wikipedia.org/wiki/Bacterial_genetic_nomenclature>`_\n- `Journal of Bacteriology \u2014 Instructions to Authors <http://jb.asm.org/site/misc/journal-ita_nom.xhtml#03>`_\n- `Human Genome Variation Society \u2014 Recommendations for the description of sequence variants <http://www.hgvs.org/mutnomen/recs.html>`_\n- `Databases cross-referenced in UniProtKB <http://www.uniprot.org/docs/dbxref>`_\n\n\n",
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        "license": "Apache",
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        "name": "gnomic",
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