{
    "info": {
        "author": "Chunlei Wu, Cyrus Afrasiabi, Sebastien Lelong",
        "author_email": "cwu@scripps.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: OS Independent",
            "Operating System :: POSIX",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Utilities"
        ],
        "description": ".. image:: https://badge.fury.io/py/myvariant.svg\n    :target: https://pypi.org/project/myvariant/\n\n.. image:: https://img.shields.io/pypi/pyversions/myvariant.svg\n    :target: https://pypi.org/project/myvariant/\n\n.. image:: https://img.shields.io/pypi/format/myvariant.svg\n    :target: https://pypi.org/project/myvariant/\n\nIntro\n=====\n\nMyVariant.Info_ provides simple-to-use REST web services to query/retrieve genetic\nvariant annotation data. It's designed with simplicity and performance emphasized.\n*myvariant*, is an easy-to-use Python wrapper to access MyVariant.Info_ services.\n\n.. _MyVariant.Info: http://myvariant.info\n.. _biothings_client: https://pypi.org/project/biothings-client/\n.. _myvariant: https://pypi.org/project/myvariant/\n\n.. Note::\n    As of v1.0.0, myvariant_ Python package is now a thin wrapper of underlying biothings_client_ package,\n    a universal Python client for all `BioThings APIs <http://biothings.io>`_, including MyVariant.info_.\n    The installation of myvariant_ will install biothings_client_ automatically. The following code snippets\n    are essentially equivalent:\n\n\n    * Continue using myvariant_ package\n\n        .. code-block:: python\n\n            In [1]: import myvariant\n            In [2]: mv = myvariant.MyVariantInfo()\n\n    * Use biothings_client_ package directly\n\n        .. code-block:: python\n\n            In [1]: from biothings_client import get_client\n            In [2]: mv = get_client('variant')\n\n    After that, the use of ``mv`` instance is exactly the same, e.g. the usage examples below.\n\n\nRequirements\n============\n    python >=2.7 (including python3)\n\n    (Python 2.6 might still work, not it's not supported any more since v4.0.0.)\n\n    biothings_client_ (>=0.2.0, install using \"pip install biothings_client\")\n\nOptional dependencies\n======================\n    `pandas <http://pandas.pydata.org>`_ (install using \"pip install pandas\") is required\n    for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.\n\nInstallation\n=============\n\n    Option 1\n          ::\n\n           pip install myvariant\n\n    Option 2\n          download/extract the source code and run::\n\n           python setup.py install\n\n    Option 3\n          install the latest code directly from the repository::\n\n            pip install -e git+https://github.com/biothings/myvariant.py#egg=myvariant\n\nVersion history\n===============\n\n    `CHANGES.txt <https://raw.githubusercontent.com/biothings/myvariant.py/master/CHANGES.txt>`_\n\nTutorial\n=========\n\n    `Access ClinVar Data from MyVariant.info Services <https://cdn.rawgit.com/biothings/myvariant.info/master/docs/ipynb/myvariant_clinvar_demo.html>`_ (the raw ipynb file is `here <https://raw.githubusercontent.com/biothings/myvariant.info/master/docs/ipynb/myvariant_clinvar_demo.ipynb>`_)\n\nDocumentation\n=============\n\n    http://myvariant-py.readthedocs.org/\n\nUsage\n=====\n\n.. code-block:: python\n\n    In [1]: import myvariant\n\n    In [2]: mv = myvariant.MyVariantInfo()\n\n    In [3]: mv.getvariant(\"chr7:g.140453134T>C\")\n    Out[3]:  #output below is collapsed\n    {\"_id\": \"chr7:g.140453134T>C\",\n     \"_version\": 1,\n     \"cadd\": {...},\n     \"cosmic\": {...},\n     \"dbnsfp\": {...},\n     \"dbsnp\": {...},\n     \"docm\": {...},\n     \"mutdb\": {...},\n     \"snpeff\": {...},\n     \"vcf\": {\n        \"alt\": \"C\",\n        \"position\": \"140453134\",\n        \"ref\": \"T\"\n     }}\n\n    In [4]: mv.getvariant(\"chr7:g.140453134T>C\", fields='cosmic,snpeff')\n    Out[4]:\n    {'_id': 'chr7:g.140453134T>C',\n     '_version': 1,\n     'snpeff': {'ann': {'transcript_biotype': 'Coding',\n       'gene_id': 'BRAF',\n       'effect': 'missense_variant',\n       'putative_impact': 'MODERATE',\n       'cds': {'length': '2301', 'position': '1801'},\n       'feature_type': 'transcript',\n       'gene_name': 'BRAF',\n       'feature_id': 'NM_004333.4',\n       'hgvs_p': 'p.Lys601Glu',\n       'hgvs_c': 'c.1801A>G',\n       'rank': '15',\n       'total': '18',\n       'protein': {'length': '766', 'position': '601'},\n       'cdna': {'length': '2946', 'position': '1862'}}},\n     'cosmic': {'mut_freq': 0.07,\n      'alt': 'G',\n      'mut_nt': 'A>G',\n      'tumor_site': 'upper_aerodigestive_tract',\n      'ref': 'A',\n      'chrom': '7',\n      'hg19': {'start': 140453134, 'end': 140453134},\n      'cosmic_id': 'COSM478'}\n     }\n\n    In [5]: mv.getvariant(\"chr7:g.140453134T>C\", fields=['cosmic.tumor_site', 'snpeff.ann.gene_name'])\n    Out[5]:\n    {'_id': 'chr7:g.140453134T>C',\n     '_version': 1,\n     'snpeff': {'ann': {'gene_name': 'BRAF'}},\n     'cosmic': {'tumor_site': 'upper_aerodigestive_tract'}\n    }\n\n    In [6]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'])\n    Out[6]:\n    [{'_id': 'chr1:g.866422C>T',\n       ...\n     },\n     {'_id': 'chr1:g.876664G>A',\n      ...\n     },\n     {'_id': 'chr1:g.69635G>C',\n      ...\n     }]\n\n    In [7]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],\n    fields='cadd.phred,dbsnp.rsid')\n    Out[7]:\n    [{'query': 'chr1:g.866422C>T',\n      '_id': 'chr1:g.866422C>T',\n      'dbsnp': {'rsid': 'rs139210662'},\n      'cadd': {'phred': 14.31}},\n     {'query': 'chr1:g.876664G>A',\n      '_id': 'chr1:g.876664G>A',\n      'dbsnp': {'rsid': 'rs571654307'},\n      'cadd': {'phred': 9.971}},\n     {'query': 'chr1:g.69635G>C',\n      '_id': 'chr1:g.69635G>C',\n      'dbsnp': {'rsid': 'rs541766448'},\n      'cadd': {'phred': 6.123}}]\n\n    In [8]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],\n    fields='cadd.phred,dbsnp.rsid', as_dataframe=True)\n    Out[8]:\n                                   _id  cadd.phred   dbsnp.rsid\n    query\n    chr1:g.866422C>T  chr1:g.866422C>T      14.310  rs139210662\n    chr1:g.876664G>A  chr1:g.876664G>A       9.971  rs571654307\n    chr1:g.69635G>C    chr1:g.69635G>C       6.123  rs541766448\n\n    In [9]: mv.query('dbsnp.rsid:rs58991260', fields='dbsnp')\n    Out[9]:\n    {'total': 1,\n     'hits': [{'_score': 17.48471,\n       '_id': 'chr1:g.218631822G>A',\n       'dbsnp': {'class': 'SNV',\n        'gmaf': 0.02157,\n        'vartype': 'snp',\n        'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],\n        'var_subtype': 'ts',\n        'alleles': [{'freq': 0.9784, 'allele': 'G'},\n         {'freq': 0.02157, 'allele': 'A'}],\n        'allele_origin': 'unspecified',\n        'chrom': '1',\n        'hg19': {'start': 218631822, 'end': 218631823},\n        'validated': True,\n        'dbsnp_build': 129,\n        'alt': 'A',\n        'rsid': 'rs58991260',\n        'ref': 'G'}}],\n     'took': 24,\n     'max_score': 17.48471}\n\n\n    In [10]: mv.query('snpeff.ann.gene_name:cdk2 AND dbnsfp.polyphen2.hdiv.pred:D',\n    fields='dbnsfp.polyphen2.hdiv')\n    Out[10]:\n    {'total': 1188,\n     'hits': [{'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,\n          'pred': 'D',\n          'score': 1.0}}},\n       '_score': 8.343648,\n       '_id': 'chr12:g.56359720C>T'},\n      {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,\n          'pred': 'D',\n          'score': [1.0, 0.957, 0.998]}}},\n       '_score': 8.343648,\n       '_id': 'chr12:g.56360819G>C'},\n\n       ...\n\n      {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,\n          'pred': 'D',\n          'score': 1.0}}},\n       '_score': 8.343648,\n       '_id': 'chr12:g.56360853G>A'}],\n       'took': 3521,\n       'max_score': 8.343648}\n\n\n    In [11]: mv.query('chr1:69000-70000', fields='cadd.phred')\n    Out[11]:\n    {'total': 3,\n     'hits': [\n      {'_score': 14.155852, '_id': 'chr1:g.69428T>G', 'cadd': {'phred': 12.14}},\n      {'_score': 14.148425, '_id': 'chr1:g.69511A>G', 'cadd': {'phred': 8.98}},\n      {'_score': 3.5420983, '_id': 'chr1:g.69538G>A', 'cadd': {'phred': 7.339}}],\n     'took': 725,\n     'max_score': 14.155852}\n\n    In [12]: mv.querymany(['rs58991260', 'rs2500'], scopes='dbsnp.rsid', fields='dbsnp')\n    Finished.\n    Out[12]:\n    [{'query': 'rs58991260',\n      '_id': 'chr1:g.218631822G>A',\n      'dbsnp': {'class': 'SNV',\n       'gmaf': 0.02157,\n       'vartype': 'snp',\n       'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],\n       'var_subtype': 'ts',\n       'alleles': [{'freq': 0.9784, 'allele': 'G'},\n        {'freq': 0.02157, 'allele': 'A'}],\n       'allele_origin': 'unspecified',\n       'chrom': '1',\n       'hg19': {'start': 218631822, 'end': 218631823},\n       'validated': True,\n       'dbsnp_build': 129,\n       'alt': 'A',\n       'rsid': 'rs58991260',\n       'ref': 'G'}},\n     {'query': 'rs2500',\n      '_id': 'chr11:g.66397320A>G',\n      'dbsnp': {'class': 'SNV',\n       'vartype': 'snp',\n       'flags': ['ASP', 'INT', 'RV', 'U3'],\n       'var_subtype': 'ts',\n       'alleles': [{'allele': 'A'}, {'allele': 'G'}],\n       'allele_origin': 'unspecified',\n       'chrom': '11',\n       'hg19': {'start': 66397320, 'end': 66397321},\n       'dbsnp_build': 36,\n       'alt': 'G',\n       'ref': 'A',\n       'rsid': 'rs2500',\n       'validated': False}}]\n\n    In [13]: mv.querymany(['RCV000083620', 'RCV000083584'],\n    scopes='clinvar.rcv_accession', fields='clinvar')\n    Finished.\n    Out[13]:\n    [{'query': 'RCV000083620',\n      'clinvar': {'type': 'single nucleotide variant',\n       'gene': {'id': 5009, 'symbol': 'OTC'},\n       'origin': 'unknown',\n       'last_evaluated': 'None',\n       'other_ids': 'dbSNP:72558473;',\n       'clinvar_id': 97371,\n       'hgvs': {'genomic': ['NG_008471.1:g.64470C>T',\n         'NC_000023.11:g.38411952C>T',\n         'NC_000023.10:g.38271205C>T'],\n        'coding': 'NM_000531.5:c.958C>T'},\n       'chrom': 'X',\n       'cytogenic': 'Xp11.4',\n       'name': 'NM_000531.5(OTC):c.958C>T (p.Arg320Ter)',\n       'number_submitters': 1,\n       'alt': 'T',\n       'hg19': {'start': 38271205, 'end': 38271205},\n       'allele_id': 103263,\n       'rcv_accession': 'RCV000083620',\n       'review_status': 'classified by single submitter',\n       'clinical_significance': 'Pathogenic',\n       'rsid': 'rs72558473',\n       'ref': 'C'},\n      '_id': 'chrX:g.38271205C>T'},\n     {'query': 'RCV000083584',\n      'clinvar': {'type': 'Deletion',\n       'gene': {'id': 5009, 'symbol': 'OTC'},\n       'origin': 'unknown',\n       'last_evaluated': 'None',\n       'other_ids': 'dbSNP:72558452;',\n       'clinvar_id': 97337,\n       'hgvs': {'genomic': ['NG_008471.1:g.61493_61495delGAG',\n         'NC_000023.11:g.38408975_38408977delGAG',\n         'NC_000023.10:g.38268228_38268230delGAG'],\n        'coding': 'NM_000531.5:c.817_819delGAG'},\n       'chrom': 'X',\n       'cytogenic': 'Xp11.4',\n       'name': 'NM_000531.5(OTC):c.817_819delGAG (p.Glu273del)',\n       'number_submitters': 1,\n       'alt': '-',\n       'hg19': {'start': 38268228, 'end': 38268230},\n       'allele_id': 103229,\n       'rcv_accession': 'RCV000083584',\n       'review_status': 'classified by single submitter',\n       'clinical_significance': 'Pathogenic',\n       'rsid': 'rs72558452',\n       'ref': 'GAG'},\n      '_id': 'chrX:g.38268228_38268230del'}]\n\n    In [14]: mv.querymany(['rs2500', 'RCV000083611', 'COSM1392449'],\n    scopes='clinvar.rcv_accession,dbsnp.rsid,cosmic.cosmic_id', fields='vcf', as_dataframe=1)\n    Finished.\n    Out[14]:\n                                  _id vcf.alt vcf.position vcf.ref\n    query\n    rs2500        chr11:g.66397320A>G       G     66397320       A\n    RCV000083611   chrX:g.38271176A>G       G     38271176       A\n    COSM1392449   chr19:g.30935013C>T       T     30935013       C\n\n\n    In [15]: mv.querymany(['rs58991260', 'rs2500', 'NA_TEST'], scopes='dbsnp.rsid', fields='dbsnp')\n    Finished.\n    1 input query terms found no hit:\n            ['NA_TEST']\n    Pass \"returnall=True\" to return complete lists of duplicate or missing query terms.\n    Out[15]:\n    [{'query': 'rs58991260',\n      '_id': 'chr1:g.218631822G>A',\n      'dbsnp': {'class': 'SNV',\n       'gmaf': 0.02157,\n       'vartype': 'snp',\n       'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],\n       'var_subtype': 'ts',\n       'alleles': [{'freq': 0.9784, 'allele': 'G'},\n        {'freq': 0.02157, 'allele': 'A'}],\n       'allele_origin': 'unspecified',\n       'chrom': '1',\n       'hg19': {'start': 218631822, 'end': 218631823},\n       'validated': True,\n       'dbsnp_build': 129,\n       'alt': 'A',\n       'rsid': 'rs58991260',\n       'ref': 'G'}},\n     {'query': 'rs2500',\n      '_id': 'chr11:g.66397320A>G',\n      'dbsnp': {'class': 'SNV',\n       'vartype': 'snp',\n       'flags': ['ASP', 'INT', 'RV', 'U3'],\n       'var_subtype': 'ts',\n       'alleles': [{'allele': 'A'}, {'allele': 'G'}],\n       'allele_origin': 'unspecified',\n       'chrom': '11',\n       'hg19': {'start': 66397320, 'end': 66397321},\n       'dbsnp_build': 36,\n       'alt': 'G',\n       'ref': 'A',\n       'rsid': 'rs2500',\n       'validated': False}},\n     {'query': 'NA_TEST', 'notfound': True}]\n\n\nContact\n========\nDrop us any question or feedback:\n    * biothings@googlegroups.com  (public discussion)\n    * help@myvariant.info (reach devs privately)\n    * `Github issues <https://github.com/biothings/myvariant.info/issues>`_\n    * on twitter `@myvariantinfo <https://twitter.com/myvariantinfo>`_\n    * Post a question on `BioStars.org <https://www.biostars.org/p/new/post/?tag_val=myvariant>`_ with tag #myvariant.\n\n\n\n",
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