Python API that consumes the biomart webservice
Project description
Python API that consumes the biomart webservice.
What it will do:
Show all databases of a biomart server
Show all datasets of a biomart database
Show attributes and filters of a biomart dataset
Run your query formatted as a Python dict.
What it won’t do:
Process and return the results as JSON,XML,etc. It will only return the Biomart response as TSV format.
Usage
Select a dataset
from biomart import BiomartDataset
interpro = BiomartDataset( "http://www.biomart.org/biomart", {'name': 'entry'} )
Use proxy
import os
interpro.http_proxy = os.environ.get('http_proxy', 'http://my_http_proxy.org')
Run query: Give me the name and abstract of interpro entry IPR027603
response = interpro.search({
'filters': {
'entry_id': 'IPR027603',
},
'attributes': [
'entry_name', 'abstract'
]
})
# Returned format is TSV
for line in response.iter_lines():
print line.split("\t")
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biomart-0.2.0.tar.gz
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