add namespace prefixes to parse uniprot XML (fixes #4)

ippisite/ippidb/ws.py

@@ -37,15 +37,16 @@ def get_epo_info(patent_number):
 
 def get_uniprot_info(uniprot_id):
     uniprot_client = UniProt()
+    ns = {'u':'http://uniprot.org/uniprot'}
     resp = uniprot_client.retrieve(uniprot_id)
-    recommended_name = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}protein/{http://uniprot.org/uniprot}recommendedName/{http://uniprot.org/uniprot}fullName')[0].text
-    organism = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}organism/{http://uniprot.org/uniprot}dbReference[@type="NCBI Taxonomy"]')[0].attrib['id']
-    gene = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}gene/{http://uniprot.org/uniprot}name[@type="primary"]')[0].text
-    entry_name = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}name')[0].text
-    go_els = resp.root.findall('{http://uniprot.org/uniprot}entry/{http://uniprot.org/uniprot}dbReference[@type="GO"]')
+    recommended_name = resp.root.findall('u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
+    organism = resp.root.findall('u:entry/u:organism/u:dbReference[@type="NCBI Taxonomy"]', ns)[0].attrib['id']
+    gene = resp.root.findall('u:entry/u:gene/u:name[@type="primary"]', ns)[0].text
+    entry_name = resp.root.findall('u:entry/u:name', ns)[0].text
+    go_els = resp.root.findall('u:entry/u:dbReference[@type="GO"]', ns)
     molecular_functions = []
     for go_el in go_els:
-        term_property_value = go_el.findall('{http://uniprot.org/uniprot}property[@type="term"]')[0].attrib['value']
+        term_property_value = go_el.findall('u:property[@type="term"]', ns)[0].attrib['value']
         if term_property_value[0:2]=='F:':
             molecular_functions.append('GO_'+go_el.attrib['id'][3:])
     return {'recommended_name': recommended_name,