From 1826224503b81ef0497f24e2c3259ce24340e930 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Sun, 26 Mar 2017 23:48:55 +0200
Subject: [PATCH] retrieve go identifiers for molecular functions from Uniprot
---
ippisite/ippidb/ws.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 8b9b3f3a..b8386de6 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -42,10 +42,17 @@ def get_uniprot_info(uniprot_id):
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"]')
+ molecular_functions = []
+ for go_el in go_els:
+ term_property_value = go_el.findall('{http://uniprot.org/uniprot}property[@type="term"]')[0].attrib['value']
+ if term_property_value[0:2]=='F:':
+ molecular_functions.append('GO_'+go_el.attrib['id'][3:])
return {'recommended_name': recommended_name,
'organism': int(organism),
'gene': gene,
- 'entry_name': entry_name
+ 'entry_name': entry_name,
+ 'molecular_functions': molecular_functions
}
def get_taxonomy_info(taxonomy_id):
--
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