From 6f375a5b48fe7743f3a5f2e50e1ed7cd0bb2ac3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 28 Mar 2017 09:00:11 +0200
Subject: [PATCH] add namespace prefixes to parse uniprot XML (fixes #4)
---
ippisite/ippidb/ws.py | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index f52d2e76..768d0afb 100644
--- a/ippisite/ippidb/ws.py
+++ b/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,
--
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