Python Client for MyGene.Info services.
Project description
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
- Option 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
Tutorial
Usage
In [1]: import mygene
In [2]: mg = mygene.MyGeneInfo()
In [3]: mg.getgene(1017)
Out[3]:
{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'symbol': 'CDK2',
'taxid': 9606}
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', 'NM_052827']},
'symbol': 'CDK2'}
In [6]: mg.getgenes([1017,1018,'ENSG00000148795'])
Out[6]:
[{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'query': '1017',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '1018',
'entrezgene': 1018,
'name': 'cyclin-dependent kinase 3',
'query': '1018',
'symbol': 'CDK3',
'taxid': 9606},
{'_id': '1586',
'entrezgene': 1586,
'name': 'cytochrome P450, family 17, subfamily A, polypeptide 1',
'query': 'ENSG00000148795',
'symbol': 'CYP17A1',
'taxid': 9606}]
In [7]: mg.query('cdk2', size=5)
Out[7]:
{'hits': [{'_id': '1017',
'_score': 373.24667,
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '12566',
'_score': 353.90176,
'entrezgene': 12566,
'name': 'cyclin-dependent kinase 2',
'symbol': 'Cdk2',
'taxid': 10090},
{'_id': '362817',
'_score': 264.88477,
'entrezgene': 362817,
'name': 'cyclin dependent kinase 2',
'symbol': 'Cdk2',
'taxid': 10116},
{'_id': '52004',
'_score': 21.221401,
'entrezgene': 52004,
'name': 'CDK2-associated protein 2',
'symbol': 'Cdk2ap2',
'taxid': 10090},
{'_id': '143384',
'_score': 18.617256,
'entrezgene': 143384,
'name': 'CDK2-associated, cullin domain 1',
'symbol': 'CACUL1',
'taxid': 9606}],
'max_score': 373.24667,
'took': 10,
'total': 28}
In [8]: mg.query('reporter:1000_at')
Out[8]:
{'hits': [{'_id': '5595',
'_score': 11.163337,
'entrezgene': 5595,
'name': 'mitogen-activated protein kinase 3',
'symbol': 'MAPK3',
'taxid': 9606}],
'max_score': 11.163337,
'took': 6,
'total': 1}
In [9]: mg.query('symbol:cdk2', species='human')
Out[9]:
{'hits': [{'_id': '1017',
'_score': 84.17707,
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'symbol': 'CDK2',
'taxid': 9606}],
'max_score': 84.17707,
'took': 27,
'total': 1}
In [10]: mg.querymany([1017, '695'], scopes='entrezgene', species='human')
querying 1-2... done.
Finished.
Out[10]:
[{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'query': '1017',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '695',
'entrezgene': 695,
'name': 'Bruton agammaglobulinemia tyrosine kinase',
'query': '695',
'symbol': 'BTK',
'taxid': 9606}]
In [11]: mg.querymany([1017, '695'], scopes='entrezgene', species=9606)
querying 1-2... done.
Finished.
Out[11]:
[{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'query': '1017',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '695',
'entrezgene': 695,
'name': 'Bruton agammaglobulinemia tyrosine kinase',
'query': '695',
'symbol': 'BTK',
'taxid': 9606}]
In [12]: mg.querymany([1017, '695', 'NA_TEST'], scopes='entrezgene', species='human')
querying 1-3...
Finished.
Out[12]:
[{'_id': '1017',
'entrezgene': 1017,
'name': 'cyclin-dependent kinase 2',
'query': '1017',
'symbol': 'CDK2',
'taxid': 9606},
{'_id': '695',
'entrezgene': 695,
'name': 'Bruton agammaglobulinemia tyrosine kinase',
'query': '695',
'symbol': 'BTK',
'taxid': 9606},
{'notfound': True, 'query': 'NA_TEST'}]
Contact
Drop us any feedback at: help@mygene.info
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