Metadata-Version: 1.1
Name: myvariant
Version: 0.1.2
Summary: Python Client for MyVariant.Info services.
Home-page: https://github.com/Network-of-BioThings/myvariant.py
Author: Chunlei Wu
Author-email: cwu@scripps.edu
License: BSD
Description: Intro
        =====
        
        MyVariant.Info_ provides simple-to-use REST web services to query/retrieve genetic variant annotation data. It's designed with simplicity and performance emphasized. *myvariant*, is an easy-to-use Python wrapper to access MyVariant.Info_ services.
        
        .. _MyVariant.Info: http://myvariant.info
        .. _requests: https://pypi.python.org/pypi/requests
        
        Requirements
        ============
            python >=2.6 (including python3)
        
            requests_ (install using "pip install requests")
        
        Optional dependencies
        ======================
            `pandas <http://pandas.pydata.org>`_ (install using "pip install pandas") is required for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.
        
        Installation
        =============
        
            Option 1
                  ::
        
                   pip install myvariant
        
            Option 2
                  download/extract the source code and run::
        
                   python setup.py install
        
            Option 3
                  install the latest code directly from the repository::
        
                    pip install -e git+https://github.com/Network-of-BioThings/myvariant.py
        
        Version history
        ===============
        
            `CHANGES.txt <https://raw.githubusercontent.com/Network-of-BioThings/myvariant.py/master/CHANGES.txt>`_
        
        Tutorial
        =========
        
        .. * 'ID mapping'_
        
        TODO
        
        Documentation
        =============
        
            http://myvariant-py.readthedocs.org/
        
        Usage
        =====
        
        .. code-block:: python
        
            In [1]: import myvariant
        
            In [2]: mv = myvariant.MyVariantInfo()
        
            In [3]: mv.getvariant("chr7:g.140453134T>C")
            Out[3]:  #output below is collapsed
            {"_id": "chr7:g.140453134T>C",
             "_version": 1,
             "cadd": {...},
             "cosmic": {...},
             "dbnsfp": {...},
             "dbsnp": {...},
             "docm": {...},
             "mutdb": {...},
             "snpeff": {...},
             "vcf": {
                "alt": "C",
                "position": "140453134",
                "ref": "T"
             }}
        
            In [4]: mv.getvariant("chr7:g.140453134T>C", fields='cosmic,snpeff')
            Out[4]:
            {'_id': 'chr7:g.140453134T>C',
             '_version': 1,
             'snpeff': {'ann': {'transcript_biotype': 'Coding',
               'gene_id': 'BRAF',
               'effect': 'missense_variant',
               'putative_impact': 'MODERATE',
               'cds': {'length': '2301', 'position': '1801'},
               'feature_type': 'transcript',
               'gene_name': 'BRAF',
               'feature_id': 'NM_004333.4',
               'hgvs_p': 'p.Lys601Glu',
               'hgvs_c': 'c.1801A>G',
               'rank': '15',
               'total': '18',
               'protein': {'length': '766', 'position': '601'},
               'cdna': {'length': '2946', 'position': '1862'}}},
             'cosmic': {'mut_freq': 0.07,
              'alt': 'G',
              'mut_nt': 'A>G',
              'tumor_site': 'upper_aerodigestive_tract',
              'ref': 'A',
              'chrom': '7',
              'hg19': {'start': 140453134, 'end': 140453134},
              'cosmic_id': 'COSM478'}
             }
        
            In [5]: mv.getvariant("chr7:g.140453134T>C", fields=['cosmic.tumor_site', 'snpeff.ann.gene_name'])
            Out[5]:
            {'_id': 'chr7:g.140453134T>C',
             '_version': 1,
             'snpeff': {'ann': {'gene_name': 'BRAF'}},
             'cosmic': {'tumor_site': 'upper_aerodigestive_tract'}
            }
        
            In [6]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'])
            Out[6]:
            [{'_id': 'chr1:g.866422C>T',
               ...
             },
             {'_id': 'chr1:g.876664G>A',
              ...
             },
             {'_id': 'chr1:g.69635G>C',
              ...
             }]
        
            In [7]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
            fields='cadd.phred,dbsnp.rsid')
            Out[7]:
            [{'query': 'chr1:g.866422C>T',
              '_id': 'chr1:g.866422C>T',
              'dbsnp': {'rsid': 'rs139210662'},
              'cadd': {'phred': 14.31}},
             {'query': 'chr1:g.876664G>A',
              '_id': 'chr1:g.876664G>A',
              'dbsnp': {'rsid': 'rs571654307'},
              'cadd': {'phred': 9.971}},
             {'query': 'chr1:g.69635G>C',
              '_id': 'chr1:g.69635G>C',
              'dbsnp': {'rsid': 'rs541766448'},
              'cadd': {'phred': 6.123}}]
        
            In [8]: mv.getvariants(['chr1:g.866422C>T', 'chr1:g.876664G>A','chr1:g.69635G>C'],
            fields='cadd.phred,dbsnp.rsid', as_dataframe=True)
            Out[8]:
                                           _id  cadd.phred   dbsnp.rsid
            query
            chr1:g.866422C>T  chr1:g.866422C>T      14.310  rs139210662
            chr1:g.876664G>A  chr1:g.876664G>A       9.971  rs571654307
            chr1:g.69635G>C    chr1:g.69635G>C       6.123  rs541766448
        
            In [9]: mv.query('dbsnp.rsid:rs58991260', fields='dbsnp')
            Out[9]:
            {'total': 1,
             'hits': [{'_score': 17.48471,
               '_id': 'chr1:g.218631822G>A',
               'dbsnp': {'class': 'SNV',
                'gmaf': 0.02157,
                'vartype': 'snp',
                'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
                'var_subtype': 'ts',
                'alleles': [{'freq': 0.9784, 'allele': 'G'},
                 {'freq': 0.02157, 'allele': 'A'}],
                'allele_origin': 'unspecified',
                'chrom': '1',
                'hg19': {'start': 218631822, 'end': 218631823},
                'validated': True,
                'dbsnp_build': 129,
                'alt': 'A',
                'rsid': 'rs58991260',
                'ref': 'G'}}],
             'took': 24,
             'max_score': 17.48471}
        
        
            In [10]: mv.query('snpeff.ann.gene_name:cdk2 AND dbnsfp.polyphen2.hdiv.pred:D',
            fields='dbnsfp.polyphen2.hdiv')
            Out[10]:
            {'total': 1188,
             'hits': [{'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
                  'pred': 'D',
                  'score': 1.0}}},
               '_score': 8.343648,
               '_id': 'chr12:g.56359720C>T'},
              {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
                  'pred': 'D',
                  'score': [1.0, 0.957, 0.998]}}},
               '_score': 8.343648,
               '_id': 'chr12:g.56360819G>C'},
        
               ...
        
              {'dbnsfp': {'polyphen2': {'hdiv': {'rankscore': 0.89865,
                  'pred': 'D',
                  'score': 1.0}}},
               '_score': 8.343648,
               '_id': 'chr12:g.56360853G>A'}],
               'took': 3521,
               'max_score': 8.343648}
        
        
            In [11]: mv.query('chr1:69000-70000', fields='cadd.phred')
            Out[11]:
            {'total': 3,
             'hits': [
              {'_score': 14.155852, '_id': 'chr1:g.69428T>G', 'cadd': {'phred': 12.14}},
              {'_score': 14.148425, '_id': 'chr1:g.69511A>G', 'cadd': {'phred': 8.98}},
              {'_score': 3.5420983, '_id': 'chr1:g.69538G>A', 'cadd': {'phred': 7.339}}],
             'took': 725,
             'max_score': 14.155852}
        
            In [12]: mv.querymany(['rs58991260', 'rs2500'], scopes='dbsnp.rsid', fields='dbsnp')
            Finished.
            Out[12]:
            [{'query': 'rs58991260',
              '_id': 'chr1:g.218631822G>A',
              'dbsnp': {'class': 'SNV',
               'gmaf': 0.02157,
               'vartype': 'snp',
               'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
               'var_subtype': 'ts',
               'alleles': [{'freq': 0.9784, 'allele': 'G'},
                {'freq': 0.02157, 'allele': 'A'}],
               'allele_origin': 'unspecified',
               'chrom': '1',
               'hg19': {'start': 218631822, 'end': 218631823},
               'validated': True,
               'dbsnp_build': 129,
               'alt': 'A',
               'rsid': 'rs58991260',
               'ref': 'G'}},
             {'query': 'rs2500',
              '_id': 'chr11:g.66397320A>G',
              'dbsnp': {'class': 'SNV',
               'vartype': 'snp',
               'flags': ['ASP', 'INT', 'RV', 'U3'],
               'var_subtype': 'ts',
               'alleles': [{'allele': 'A'}, {'allele': 'G'}],
               'allele_origin': 'unspecified',
               'chrom': '11',
               'hg19': {'start': 66397320, 'end': 66397321},
               'dbsnp_build': 36,
               'alt': 'G',
               'ref': 'A',
               'rsid': 'rs2500',
               'validated': False}}]
        
            In [13]: mv.querymany(['RCV000083620', 'RCV000083584'],
            scopes='clinvar.rcv_accession', fields='clinvar')
            Finished.
            Out[13]:
            [{'query': 'RCV000083620',
              'clinvar': {'type': 'single nucleotide variant',
               'gene': {'id': 5009, 'symbol': 'OTC'},
               'origin': 'unknown',
               'last_evaluated': 'None',
               'other_ids': 'dbSNP:72558473;',
               'clinvar_id': 97371,
               'hgvs': {'genomic': ['NG_008471.1:g.64470C>T',
                 'NC_000023.11:g.38411952C>T',
                 'NC_000023.10:g.38271205C>T'],
                'coding': 'NM_000531.5:c.958C>T'},
               'chrom': 'X',
               'cytogenic': 'Xp11.4',
               'name': 'NM_000531.5(OTC):c.958C>T (p.Arg320Ter)',
               'number_submitters': 1,
               'alt': 'T',
               'hg19': {'start': 38271205, 'end': 38271205},
               'allele_id': 103263,
               'rcv_accession': 'RCV000083620',
               'review_status': 'classified by single submitter',
               'clinical_significance': 'Pathogenic',
               'rsid': 'rs72558473',
               'ref': 'C'},
              '_id': 'chrX:g.38271205C>T'},
             {'query': 'RCV000083584',
              'clinvar': {'type': 'Deletion',
               'gene': {'id': 5009, 'symbol': 'OTC'},
               'origin': 'unknown',
               'last_evaluated': 'None',
               'other_ids': 'dbSNP:72558452;',
               'clinvar_id': 97337,
               'hgvs': {'genomic': ['NG_008471.1:g.61493_61495delGAG',
                 'NC_000023.11:g.38408975_38408977delGAG',
                 'NC_000023.10:g.38268228_38268230delGAG'],
                'coding': 'NM_000531.5:c.817_819delGAG'},
               'chrom': 'X',
               'cytogenic': 'Xp11.4',
               'name': 'NM_000531.5(OTC):c.817_819delGAG (p.Glu273del)',
               'number_submitters': 1,
               'alt': '-',
               'hg19': {'start': 38268228, 'end': 38268230},
               'allele_id': 103229,
               'rcv_accession': 'RCV000083584',
               'review_status': 'classified by single submitter',
               'clinical_significance': 'Pathogenic',
               'rsid': 'rs72558452',
               'ref': 'GAG'},
              '_id': 'chrX:g.38268228_38268230del'}]
        
            In [14]: mv.querymany(['rs2500', 'RCV000083611', 'COSM1392449'],
            scopes='clinvar.rcv_accession,dbsnp.rsid,cosmic.cosmic_id', fields='vcf', as_dataframe=1)
            Finished.
            Out[14]:
                                          _id vcf.alt vcf.position vcf.ref
            query
            rs2500        chr11:g.66397320A>G       G     66397320       A
            RCV000083611   chrX:g.38271176A>G       G     38271176       A
            COSM1392449   chr19:g.30935013C>T       T     30935013       C
        
        
            In [15]: mv.querymany(['rs58991260', 'rs2500', 'NA_TEST'], scopes='dbsnp.rsid', fields='dbsnp')
            Finished.
            1 input query terms found no hit:
                    ['NA_TEST']
            Pass "returnall=True" to return complete lists of duplicate or missing query terms.
            Out[15]:
            [{'query': 'rs58991260',
              '_id': 'chr1:g.218631822G>A',
              'dbsnp': {'class': 'SNV',
               'gmaf': 0.02157,
               'vartype': 'snp',
               'flags': ['ASP', 'G5', 'G5A', 'GNO', 'KGPhase1', 'KGPhase3', 'SLO'],
               'var_subtype': 'ts',
               'alleles': [{'freq': 0.9784, 'allele': 'G'},
                {'freq': 0.02157, 'allele': 'A'}],
               'allele_origin': 'unspecified',
               'chrom': '1',
               'hg19': {'start': 218631822, 'end': 218631823},
               'validated': True,
               'dbsnp_build': 129,
               'alt': 'A',
               'rsid': 'rs58991260',
               'ref': 'G'}},
             {'query': 'rs2500',
              '_id': 'chr11:g.66397320A>G',
              'dbsnp': {'class': 'SNV',
               'vartype': 'snp',
               'flags': ['ASP', 'INT', 'RV', 'U3'],
               'var_subtype': 'ts',
               'alleles': [{'allele': 'A'}, {'allele': 'G'}],
               'allele_origin': 'unspecified',
               'chrom': '11',
               'hg19': {'start': 66397320, 'end': 66397321},
               'dbsnp_build': 36,
               'alt': 'G',
               'ref': 'A',
               'rsid': 'rs2500',
               'validated': False}},
             {'query': 'NA_TEST', 'notfound': True}]
        
        
        Contact
        ========
        Drop us any feedback at: help@myvariant.info or on twitter `@myvariantinfo <https://twitter.com/myvariantinfo>`_.
        
Keywords: biology variant annotation web service client api myvariant
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Utilities
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
