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            "Development Status :: 3 - Alpha",
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            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "gene_map\n========\n\n|PyPI| |Build Status| |codecov|\n\nTool for converting between various gene ids.\n\nInstallation\n------------\n\n.. code:: bash\n\n   $ pip install gene_map\n\nUsage\n-----\n\n.. code:: bash\n\n   $ gene_map --help\n   Usage: gene_map [OPTIONS]\n\n     Map gene ids between various formats.\n\n   Options:\n     -i, --input TEXT                If it exists, treated as file with\n                                     whitespace-separated gene ids. Otherwise\n                                     treated as a gene id itself.  [required]\n     --from TEXT                     Source ID type.  [required]\n     --to TEXT                       Target ID type.  [required]\n     -o, --output FILENAME           CSV-file to save result to.\n     --organism [ARATH_3702|CAEEL_6239|CHICK_9031|DANRE_7955|DICDI_44689|DROME_7227|ECOLI_83333|HUMAN_9606|MOUSE_10090|RAT_10116|SCHPO_284812|YEAST_559292]\n                                     Organism to convert IDs in.\n     --cache-dir DIRECTORY           Folder to store ID-databases in.\n     -q, --quiet                     Suppress logging of mapping-statistics.\n     --force-download                Force download of mapping-database.\n     --help                          Show this message and exit.\n\nGetting started\n---------------\n\nCommandline usage\n~~~~~~~~~~~~~~~~~\n\nInputs can be either gene ids or files containing whitespace-separated\ngene ids:\n\n.. code:: bash\n\n   $ cat mygenes.txt\n   P63244 P08246\n   P68871\n   $ gene_map \\\n       -i P35222 -i InvalidID -i mygenes.txt -i P04637 \\\n       --from ACC --to Gene_Name \\\n       -o gene_mapping.csv\n   Mapped 5/6 genes.\n   $ cat gene_mapping.csv\n   ID_from,ID_to\n   P04637,TP53\n   P08246,ELANE\n   P35222,CTNNB1\n   P63244,RACK1\n   P68871,HBB\n\nIt is also possible to simply try to convert all given inputs without\nknowing their ID type, by using ``--from auto``:\n\n.. code:: bash\n\n   $ gene_map \\\n       -i P35222 \\\n       -i TP53 \\\n       -i '9606.ENSP00000306407' \\\n       --from auto \\\n       --to GeneID\n   Mapped 3/3 genes.\n   ID_from,ID_to\n   9606.ENSP00000306407,79007\n   P35222,1499\n   TP53,7157\n\nAttention: if an ID is valid for multiple types, unintended side-effects\nmay occur. Furthermore, all IDs are treated as strings.\n\nAPI usage\n~~~~~~~~~\n\n.. code:: python\n\n   >>> from gene_map import GeneMapper\n\n   >>> stringdb_ids = ['9606.ENSP00000306407', '9606.ENSP00000337461']\n   >>> gm = GeneMapper()  # defaults to HUMAN_9606\n   >>> gm.query(stringdb_ids, source_id_type='STRING', target_id_type='GeneID')\n   #                ID_from  ID_to\n   #0  9606.ENSP00000306407  79007\n   #1  9606.ENSP00000337461  90529\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/gene_map.svg?style=flat\n   :target: https://pypi.python.org/pypi/gene_map\n.. |Build Status| image:: https://img.shields.io/travis/kpj/gene_map.svg?style=flat\n   :target: https://travis-ci.org/kpj/gene_map\n.. |codecov| image:: https://codecov.io/gh/kpj/gene_map/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/kpj/gene_map",
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