From 7d3a131800a8ed55e86992d88735a69e9df0fe42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Tue, 7 Nov 2017 16:41:31 +0100
Subject: [PATCH] protein short name is first part of entry name (split on '_')
as ruled by O. Sperandio...
Former-commit-id: ab8b4864ee61689d00b3d86513aca8d3ffdccd2f
---
ippisite/ippidb/ws.py | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index c7341d59..7f699d49 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -49,6 +49,9 @@ def get_uniprot_info(uniprot_id):
uniprot_client = UniProt()
ns = {'u': 'http://uniprot.org/uniprot'}
resp = uniprot_client.retrieve(uniprot_id)
+ f = open('/tmp/'+uniprot_id+'.xml','w')
+ f.write(str(resp))
+ f.close()
recommended_name = resp.root.findall(
'u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
organism = resp.root.findall(
@@ -67,6 +70,7 @@ def get_uniprot_info(uniprot_id):
'organism': int(organism),
'gene': gene,
'entry_name': entry_name,
+ 'short_name': entry_name.split('_')[0],
'molecular_functions': molecular_functions
}
--
GitLab