mygene 0.1.0

Python Client for MyGene.Info services.

Intro

MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It’s designed with simplicity and performance emphasized. mygene, is an easy-to-use Python wrapper to access MyGene.Info services.

Requirements

httplib2 (install using “pip install httplib2”)

Installation

Option 1

pip install mygene

Options 2

download/extract the source code and run::

python setup install

Option 3

install the latest code directly from the repository::

pip install -e hg+https://bitbucket.org/newgene/mygene#egg=mygene

Usage

In [1]: import mygene

In [2]: mg = mygene.MyGeneInfo()

In [3]: mg.getgene(1017)
Out[3]: {'_id': '1017', 'name': 'cyclin-dependent kinase 2', 'symbol': 'CDK2'}

In [4]: mg.getgene(1017, 'name,symbol,refseq')
Out[4]:
{'_id': '1017',
 'name': 'cyclin-dependent kinase 2',
 'refseq': {'genomic': ['AC_000144.1',
   'NC_000012.11',
   'NG_028086.1',
   'NT_029419.12',
   'NW_001838059.1'],
  'protein': ['NP_001789.2', 'NP_439892.2'],
  'rna': ['NM_001798.3', 'NM_052827.2']},
 'symbol': 'CDK2'}

In [5]: mg.getgene(1017, 'name,symbol,refseq.rna')
Out[5]:
{'_id': '1017',
 'name': 'cyclin-dependent kinase 2',
 'refseq': {'rna': ['NM_001798.3', 'NM_052827.2']},
 'symbol': 'CDK2'}


In [6]: mg.getgenes([1017,1018,'ENSG00000148795'])
Out[6]:
[{'_id': '1017', 'name': 'cyclin-dependent kinase 2', 'symbol': 'CDK2'},
 {'_id': '1018', 'name': 'cyclin-dependent kinase 3', 'symbol': 'CDK3'},
 {'_id': '1586',
  'name': 'cytochrome P450, family 17, subfamily A, polypeptide 1',
  'symbol': 'CYP17A1'}]


In [7]:  mg.query('cdk2', limit=5)
Out[7]:
{'etag': '1358e787924ddb',
 'limit': 5,
 'rows': [{'id': '684247',
   'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
   'score': 2.615727663040161,
   'symbol': 'LOC684247',
   'taxid': 10116},
  {'id': '681208',
   'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
   'score': 2.288761615753174,
   'symbol': 'LOC681208',
   'taxid': 10116},
  {'id': '690181',
   'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
   'score': 2.288761615753174,
   'symbol': 'LOC690181',
   'taxid': 10116},
  {'id': '690646',
   'name': 'similar to S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (F-box/WD-40 protein 1) (FWD1)',
   'score': 1.9617958068847656,
   'symbol': 'LOC690646',
   'taxid': 10116},
  {'id': '687002',
   'name': 'similar to S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (F-box/WD-40 protein 1) (FWD1)',
   'score': 1.9617958068847656,
   'symbol': 'LOC687002',
   'taxid': 10116}],
 'skip': 0,
 'total_rows': 29}

In [8]: mg.query('reporter:1000_at')
Out[8]:
{'etag': '13574eee908e81',
 'limit': 25,
 'rows': [{'homologene': {'genes': [[9606, 5595],
     [10090, 26417],
     [10116, 50689],
     [7955, 399480],
     [3702, 837559],
     [3702, 842248]],
    'id': 55682},
   'id': '5595',
   'name': 'mitogen-activated protein kinase 3',
   'score': 8.231849670410156,
   'symbol': 'MAPK3',
   'taxid': 9606}],
 'skip': 0,
 'total_rows': 1}

In [9]: mg.query('symbol:cdk2 AND species:human')
Out[9]:
{'etag': '1358e787924ddb',
 'limit': 25,
 'rows': [{'homologene': {'genes': [[9606, 1017],
     [10090, 12566],
     [10116, 362817],
     [7227, 42453],
     [7955, 406715],
     [3702, 824036]],
    'id': 74409},
   'id': '1017',
   'name': 'cyclin-dependent kinase 2',
   'score': 71.34159851074219,
   'symbol': 'CDK2',
   'taxid': 9606}],
 'skip': 0,
 'total_rows': 1}



In [10]: mg.findgenes([1017, '695'], scope='entrezgene', species='human')
querying 1-2...
Finished.
Out[10]:
[(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
 ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase')]

In [11]: mg.findgenes([1017, '695'], scope='entrezgene', species=9606)
querying 1-2...
Finished.
Out[11]:
[(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
 ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase')]

In [12]: mg.findgenes([1017, '695', 'NA_TEST'], scope='entrezgene', species='human')
querying 1-3...
Finished.
1 input ids found no hit:
     ['NA_TEST']
Out[12]:
[(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
 ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase'),
 ('NA_TEST', '', '', '')]

In [13]: mg.findgenes([1017, '695', 'NA_TEST'], scope='entrezgene', species='human', raw=True)
querying 1-3...
Finished.
Out[13]:
[{'homologene': {'genes': [[9606, 1017],
                           [10090, 12566],
                           [10116, 362817],
                           [7227, 42453],
                           [7955, 406715],
                           [3702, 824036]],
                  'id': 74409},
  'id': '1017',
  'key': ['1017', 'entrezgene'],
  'name': 'cyclin-dependent kinase 2',
  'symbol': 'CDK2',
  'taxid': 9606},
 {'homologene': {'genes': [[9606, 695],
                           [10090, 12229],
                           [10116, 367901],
                           [7955, 568653]],
                 'id': 30953},
  'id': '695',
  'key': ['695', 'entrezgene'],
  'name': 'Bruton agammaglobulinemia tyrosine kinase',
  'symbol': 'BTK',
  'taxid': 9606}]

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