Thursday, July 1, 2010

Feature download


def download_feature(genome='H_sapiens',version='H_sapiens_Feb_2009',chromosome='chr1',datatype='refseq',format='brs'):
URL = 'http://netaffxdas.affymetrix.com/das2/genome'
affy = DAS2Sources(URL)
feature_url = ''.join((affy.prop_base,affy.capability('H_sapiens','H_sapiens_Feb_2009','features')))

segment_url = ''.join((affy.prop_base,affy.capability('H_sapiens','H_sapiens_Feb_2009','segments')))
segment_query = "segment="+'/'.join((segment_url,chromosome))

type_url = ''.join((affy.prop_base,affy.capability('H_sapiens','H_sapiens_Feb_2009','types')))
type_query = "type="+'/'.join((segment_url,datatype))

format_query='format='+format

query_param = encode_url(';'.join((segment_query,type_query,format_query)))

return '?'.join((feature_url,query_param))

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