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ariutta/getWPData.py

Last active December 17, 2015 23:49
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getWPData.py
from lxml import etree
import StringIO
tree = etree.parse("http://www.wikipathways.org/wpi/webservice/webservice.php/getPathway?pwId=WP1266")
apiResponse = tree.xpath('/ns1:getPathwayResponse/ns1:pathway/ns2:gpml', namespaces={'ns1': 'http://www.wso2.org/php/xsd','ns2': 'http://www.wikipathways.org/webservice'})
pathwayXml = StringIO.StringIO(apiResponse[0].text)
pathwayTree = etree.parse(pathwayXml)
species = pathwayTree.xpath('/foo:Pathway/@Organism', namespaces={'foo': 'http://genmapp.org/GPML/2008a'})
ids = pathwayTree.xpath('/foo:Pathway/foo:DataNode[@Type="Protein" or @Type="GeneProduct"]/foo:Xref/@ID[normalize-space() and not(ancestor::a | ancestor::script | ancestor::style)]', namespaces={'foo': 'http://genmapp.org/GPML/2008a'})
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