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        "author": "Greene Lab",
        "author_email": "team@greenelab.com",
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        "classifiers": [
            "Environment :: Web Environment",
            "Framework :: Django",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "Genes\n*****\n\nGenes is a Django app to represent genes.\n\n\nDownload and Install\n====================\n\nThis package is registered as ``django-genes`` in PyPI and is pip\ninstallable:\n\n::\n\n   pip install django-genes\n\nIf any of the following dependency packages are not found on your\nsystem, ``pip`` will install them too:\n\n* ``django 1.8 or later`` (Django web framework)\n\n* ``django-organisms`` (``Organisms`` model, which is required by\n  ``Genes`` model)\n\n* ``django-haystack`` (see ``Search Indexes and Data Template``\n  section.)\n\n* ``django-fixtureless`` (for unittest, see ``tests.py``)\n\n\nQuick Start\n===========\n\n1. Add **'genes'** and **'organisms'** to your ``INSTALLED_APPS``\nsetting like this:\n\n::\n\n   INSTALLED_APPS = (\n       ...\n       'organisms',\n       'genes',\n   )\n\n2. Run ``python manage.py migrate`` command to create ``genes`` and\n``organisms`` models.\n\n3. **(Optional)** The following step is only needed if you have\ndjango-tastypie installed to create a REST API for your project and\nwould like to have API endpoints for ``django-organisms`` and\n``django-genes``.\n\nAdd the following to your project's ``urls.py`` file:\n\n::\n\n   # There are probably already other imports here, such as:\n   # from django.conf.urls import url, patterns, include\n\n   # If you have not already done so, import the tastypie API:\n   from tastypie.api import Api\n\n   # Import the API Resources for Organisms and Genes:\n   from organisms.api import OrganismResource\n   from genes.api import GeneResource\n\n   # If you have not already done so, initialize your API and\n   # add the Organism and Gene Resources to it. You can also register\n   # the CrossRefResource and CrossRefDBResource if you want to have\n   # API endpoints for them as well.\n   v0_api = Api()\n   v0_api.register(OrganismResource())\n   v0_api.register(GeneResource())\n   v0_api.register(CrossRefResource())\n   v0_api.register(CrossRefDBResource())\n\n   # In the urlpatterns, include the urls for this api:\n   urlpatterns = patterns('',\n       ...\n       (r'^api/', include(v0_api.urls))\n   )\n\n\nSearch Indexes and Data Template\n================================\n\nThe module ``search_indexes.py`` can be used by **django haystack**\n(https://github.com/django-haystack/django-haystack) to search genes.\nIt includes the Gene fields that should be included in the search\nindex, and how they should be weighted. The ``text`` field refers to a\ndocument that is built for the search engine to index. The location of\ndata template for this document is:\n``genes/templates/search/indexes/gene_text.txt``.\n\nFor more information, see:\nhttp://django-haystack.readthedocs.org/en/latest/tutorial.html#handling-data\n\n\nUsage of Management Commands\n============================\n\nThis app includes five management commands in ``management/commands/``\nsub-directory:\n\n\n1. genes_add_xrdb\n-----------------\n\n..\n\n   This command adds cross-reference databases for genes. It **must**\n   be called for every new cross-reference database to populate the\n   gene and cross-reference objects in the database. It requires 2\n   arguments:\n\n   * name: the name of the database\n\n   * URL: the URL for that database, with the string '_REPL_' added at\n     the end of the URL\n\n   For example, this command adds Ensembl as a cross-reference\n   database:\n\n   ::\n\n      python manage.py genes_add_xrdb --name=Ensembl --URL=http://www.ensembl.org/Gene/Summary?g=_REPL_\n\n   And this command adds MIM as a cross-reference database:\n\n   ::\n\n      python manage.py genes_add_xrdb --name=MIM --URL=http://www.ncbi.nlm.nih.gov/omim/_REPL_\n\n\n2. genes_load_geneinfo\n----------------------\n\n..\n\n   This command parses gene info file(s) and saves the corresponding\n   gene objects into the database. It takes 2 required arguments and 5\n   optional arguments:\n\n   * (Required) geneinfo_file: location of gene info file;\n\n   * (Required) taxonomy_id: taxonomy ID for organism for which genes\n     are being populated;\n\n   * (Optional) gi_tax_id: alternative taxonomy ID for some organisms\n     (such as S. cerevisiae);\n\n   * (Optional) symbol_col: symbol column in gene info file. Default\n     is 2;\n\n   * (Optional) systematic_col: systematic column in gene info file.\n     Default is 3;\n\n   * (Optional) alias_col: the column containing gene aliases. If a\n     hyphen '-' or blank space ' ' is passed, symbol_col will be used.\n     Default is 4.\n\n   * (Optional) put_systematic_in_xrdb: name of cross-reference\n     Database for which you want to use organism systematic IDs as\n     CrossReference IDs. This is useful for Pseudomonas, for example,\n     as systematic IDs are saved into PseudoCAP cross-reference\n     database.\n\n   The following example shows how to download a gzipped human gene\n   info file from NIH FTP server, and populate the database based on\n   this file.\n\n   ::\n\n      # Create a temporary data directory:\n      mkdir data\n\n      # Download a gzipped human gene info file into data directory:\n      wget -P data/ -N ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz\n\n      # Unzip downloaded file:\n      gunzip -c data/Homo_sapiens.gene_info.gz > data/Homo_sapiens.gene_info\n\n      # Call genes_load_geneinfo to populate the database:\n      python manage.py genes_load_geneinfo --geneinfo_file=data/Homo_sapiens.gene_info --taxonomy_id=9606 --systematic_col=3 --symbol_col=2\n\n\n3. genes_load_uniprot.py\n------------------------\n\n..\n\n   This command can be used to populate database with UniProtKB\n   identifiers. It takes one argument:\n\n   * uniprot_file: location of a file mapping UniProtKB IDs to Entrez\n     and Ensembl IDs\n\n   **Important:** Before calling this command, please make sure that\n   both Ensembl and Entrez identifiers have been loaded into the\n   database.\n\n   After downloading the gzipped file, use ``zgrep`` command to get\n   the lines we need (the original file is quite large), then run this\n   command:\n\n   ::\n\n      wget -P data/ -N ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz\n      zgrep -e \"GeneID\" -e \"Ensembl\" data/idmapping.dat.gz > data/uniprot_entrez_ensembl.txt\n      python manage.py genes_load_uniprot --uniprot_file=data/uniprot_entrez_ensembl.txt\n\n\n4. genes_load_wb.py\n-------------------\n\n..\n\n   This command can be used to populate database with WormBase\n   identifiers. It takes 3 arguments:\n\n   * (Required) wb_url: URL of wormbase xrefs file;\n\n   * (Optional) db_name: the name of the cross-reference database,\n     default is 'WormBase'.\n\n   As is expected, the WormBase cross-reference database should be\n   populated using the ``genes_add_xrdb`` command (see command #1)\n   before this command to populate the WormBase identifiers. Here is\n   an example:\n\n   ::\n\n      # Find latest version of WormBase here:\n      # http://www.wormbase.org/about/release_schedule#102--10-1\n      python manage.py genes_load_wb --wb_url=ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS243.xrefs.txt.gz\n\n\n5. genes_load_gene_history.py\n-----------------------------\n\n..\n\n   This management command will read an input gene history file and\n   find all genes whose tax_id match input taxonomy ID. If the gene\n   already exists in the database, the Gene record in database will be\n   set as obsolete; if not, a new obsolete Gene record will be created\n   in the database.\n\n   The command accepts 2 required arguments and 3 optional arguments:\n\n   * (Required) gene_history_file: Input gene history file. A gzipped\n     example file can be found at:\n     ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz\n\n   * (Required) tax_id: Taxonomy ID assigned by NCBI to a certain\n     organism. Genes of the other organisms in input file will be\n     skipped.\n\n   * (Optional) tax_id_col: column number of tax_id in input file.\n     Default is 1.\n\n   * (Optional) discontinued_id_col: column number of discontinued\n     GeneID in input file. Default is 3.\n\n   * (Optional) discontinued_symbol_col: column number of gene's\n     discontinued symbol in input file. Default is 4.\n\n   Note that column numbers in the last three arguments all start from\n   1, **not** 0.\n\n   For example, to add obsolete genes whose tax_id is 208964 in the\n   file \"gene_history\", we will use the command like this:\n\n   ::\n\n      # Download file into your data directory:\n      cd /data_dir; wget ftp://ftp.ncbi.nih.gov/gene/DATA/gene_history.gz\n\n      # Unzip the downloaded file into \"gene_history\"\n      gunzip gene_history.gz\n\n      # Run management command:\n      python manage.py genes_load_gene_history /data_dir/gene_history 208964 --tax_id_col=1 --discontinued_id_col=3 --discontinued_symbol_col=4\n\n   (Here ``--tax_id_col=1 --discontinued_id_col=3\n   --discontinued_symbol_col=4`` are optional because they are using\n   default values.)",
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