From f9dede09b827c75718f6df786d27c54158b18c9c 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 22:23:20 +0200
Subject: [PATCH] add pfam information service client
---
ippisite/ippidb/ws.py | 15 +++++++++++++--
1 file changed, 13 insertions(+), 2 deletions(-)
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index 768d0afb..2c178fc1 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -1,6 +1,6 @@
from bioservices.eutils import EUtils
from bioservices.uniprot import UniProt
-from xml.etree.ElementTree import register_namespace
+import xml.etree.ElementTree as ET
import requests
def get_pubmed_info(pmid):
@@ -66,4 +66,15 @@ def get_taxonomy_info(taxonomy_id):
eu = EUtils()
r = eu.EFetch('taxonomy', taxonomy_id, retmode='dict')
scientific_name = r['TaxaSet']['Taxon']['ScientificName']
- return {'scientific_name': scientific_name}
+ return {'scientific_name': scientific_name}
+
+def get_pfam_info(pfam_acc):
+ resp = requests.get('http://pfam.xfam.org/family/{}?output=xml'.format(pfam_acc))
+ root = ET.fromstring(resp.text)
+ ns = {'pfam': 'http://pfam.xfam.org/'}
+ entry = root.findall('pfam:entry', ns)[0]
+ pfam_id = entry.attrib['id']
+ description = entry.findall('pfam:description', ns)[0].text.strip()
+ domain_family = ''
+ return {'id': pfam_id,
+ 'description': description}
--
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