diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index c254f2967866aa0006d4fedb0c5709edae5a6e2f..6714580e6e21422f3d9c4430640067fb9d76432a 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -188,6 +188,7 @@ class Protein(AutoFillableModel):
entry_name = models.CharField('Entry name', max_length=30)
organism = models.ForeignKey('Taxonomy', models.CASCADE)
molecular_functions = models.ManyToManyField(MolecularFunction)
+ domains = models.ManyToManyField('Domain')
@transaction.atomic
def autofill(self):
@@ -208,6 +209,7 @@ class Protein(AutoFillableModel):
taxonomy.save(autofill=True)
self.organism = taxonomy
super(Protein, self).save()
+
for go_id in info['molecular_functions']:
try:
mol_function = MolecularFunction.objects.get(go_id=go_id)
@@ -217,6 +219,15 @@ class Protein(AutoFillableModel):
mol_function.save(autofill=True)
self.molecular_functions.add(mol_function)
+ for domain_id in info['domains']:
+ try:
+ domain = Domain.objects.get(pfam_acc=domain_id)
+ except MolecularFunction.DoesNotExist:
+ domain = Domain()
+ domain.pfam_acc = domain_id
+ domain.save(autofill=True)
+ self.domains.add(domain)
+
def is_autofill_done(self):
return len(self.gene_name) > 0
@@ -231,7 +242,7 @@ class Domain(AutoFillableModel):
pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
pfam_description = models.CharField('Pfam Description', max_length=100)
- domain_family = models.CharField('Domain family', max_length=25)
+ domain_family = models.CharField('Domain family', max_length=25, blank=True, default="")
# TODO: what is this field? check database
# contents
diff --git a/ippisite/ippidb/tests.py b/ippisite/ippidb/tests.py
index 5fc938e61a76b2964a8eeab772b14e58a057d1e0..5b0ff4b7017fb1f64046ba28d0f24b7b75c29449 100644
--- a/ippisite/ippidb/tests.py
+++ b/ippisite/ippidb/tests.py
@@ -4,15 +4,18 @@ iPPI-DB unit tests
import re
+from django.core.management import call_command
from django.test import TestCase
from django.urls import reverse
-from django.core.management import call_command
from openbabel import vectorUnsignedInt, OBFingerprint
+from ippidb import ws
+from ippidb.ws import get_uniprot_info
from .models import Compound, CompoundTanimoto, create_tanimoto
-from .models import DrugBankCompound, DrugbankCompoundTanimoto
+from .models import DrugBankCompound
from .utils import FingerPrinter, mol2smi, smi2mol, smi2inchi, smi2inchikey
+
class MolSmiTestCase(TestCase):
"""
Test MOL to SMILES and SMILES to MOL format conversion functions
@@ -322,3 +325,71 @@ class QuestionCompoundViews(TestCase):
url = reverse('compound_list')
response = self.client.get(url)
self.assertEqual(response.status_code, 200)
+
+
+class TestGetUniprotInfo(TestCase):
+ """
+ Test retrieving information for a uniprot entry
+ """
+
+ def test_get_uniprot_info(self):
+ resp = get_uniprot_info('Q15286')
+ self.assertEqual(resp['recommended_name'],'Ras-related protein Rab-35')
+ self.assertEqual(resp['organism'],9606)
+ self.assertEqual(resp['gene_id'],11021)
+ exp_gene_names = [{'name': 'RAB35', 'type': 'primary'}, {'name': 'RAB1C', 'type': 'synonym'}, {'name': 'RAY', 'type': 'synonym'}]
+ self.assertEqual(sorted(resp['gene_names'], key=lambda k: k['name']), sorted(exp_gene_names, key=lambda k: k['name']))
+ self.assertEqual(resp['entry_name'],'RAB35_HUMAN')
+ self.assertEqual(resp['short_name'],'RAB35')
+ exp_molecular_functions = ['GO_0003924', 'GO_0005525', 'GO_0005546', 'GO_0019003']
+ self.assertEqual(sorted(resp['molecular_functions']),sorted(exp_molecular_functions))
+ exp_cellular_localisations = ['GO_0000139', 'GO_0005829', 'GO_0005886', 'GO_0005905', 'GO_0010008',
+ 'GO_0030665', 'GO_0031253', 'GO_0042470', 'GO_0045171', 'GO_0045334',
+ 'GO_0055038', 'GO_0070062', 'GO_0098993']
+ self.assertEqual(sorted(resp['cellular_localisations']),sorted(exp_cellular_localisations))
+ exp_biological_processes = ['GO_0000281', 'GO_0006886', 'GO_0008104', 'GO_0016197',
+ 'GO_0019882', 'GO_0031175', 'GO_0032456', 'GO_0032482',
+ 'GO_0036010', 'GO_0048227', 'GO_1990090']
+ self.assertEqual(sorted(resp['biological_processes']),sorted(exp_biological_processes))
+ exp_accessions = ['Q15286', 'B2R6E0', 'B4E390']
+ self.assertEqual(sorted(resp['accessions']),sorted(exp_accessions))
+ exp_citations = [
+ {'doi': '10.1006/bbrc.1994.2889', 'pmid': '7811277'},
+ {'doi': '10.1038/ng1285', 'pmid': '14702039'},
+ {'doi': '10.1038/nature04569', 'pmid': '16541075'},
+ {'doi': '10.1101/gr.2596504', 'pmid': '15489334'},
+ {'doi': '10.1016/j.cub.2006.07.020', 'pmid': '16950109'},
+ {'doi': '10.1021/pr060363j', 'pmid': '17081065'},
+ {'doi': '10.1074/jbc.M109.050930', 'pmid': '20154091'},
+ {'doi': '10.1186/1752-0509-5-17', 'pmid': '21269460'},
+ {'doi': '10.1038/nature10335', 'pmid': '21822290'},
+ {'doi': '10.1038/emboj.2012.16', 'pmid': '22307087'},
+ {'doi': '10.1111/j.1600-0854.2011.01294.x', 'pmid': '21951725'},
+ {'doi': '10.1021/pr300630k', 'pmid': '23186163'},
+ {'doi': '10.1002/pmic.201400617', 'pmid': '25944712'},
+ {'doi': '10.1073/pnas.1110415108', 'pmid': '22065758'}
+ ]
+ self.assertEqual(sorted(exp_citations, key=lambda k: k['pmid']), sorted(resp['citations'], key=lambda k: k['pmid']))
+ exp_alternative_names = [{'full': 'GTP-binding protein RAY'}, {'full': 'Ras-related protein Rab-1C'}]
+ self.assertEqual(sorted(exp_alternative_names, key=lambda k: k['full']), sorted(resp['alternative_names'], key=lambda k: k['full']))
+
+ def test_get_uniprot_info_domains(self):
+ resp = get_uniprot_info('O00255')
+ exp_domains = ['PF05053']
+ self.assertEqual(sorted(resp['domains']), sorted(exp_domains))
+
+
+class TestGetPDBUniProtMapping(TestCase):
+ """
+ Test retrieving protein for a PDB entry
+ """
+
+ def test_find_info(self):
+ target = sorted(['Q03164', 'O00255'])
+ resp = ws.get_pdb_uniprot_mapping('3u85')
+ resp = sorted(resp)
+ self.assertEqual(resp, target)
+ self.assertEqual(len(resp), len(set(resp)))
+
+ def test_entry_not_found(self):
+ self.assertRaises(ws.EntryNotFoundError, ws.get_pdb_uniprot_mapping, 'Xu85')
diff --git a/ippisite/ippidb/ws.py b/ippisite/ippidb/ws.py
index ae59dcdc87a4e86c0ac7fe91dd223614b2dbb413..67ccbeab34e0b9d8f43214a1596333ad22ec0de1 100644
--- a/ippisite/ippidb/ws.py
+++ b/ippisite/ippidb/ws.py
@@ -1,6 +1,7 @@
"""
iPPI-DB web-service client utility functions
"""
+
import json
import xml.etree.ElementTree as ET
@@ -10,7 +11,14 @@ from bioservices.uniprot import UniProt
from bs4 import BeautifulSoup
-class BibliographicalEntryNotFound(Exception):
+class EntryNotFoundError(Exception):
+
+ def __init__(self, entry_id):
+ self.entry_id = entry_id
+ super().__init__('%s not found' % entry_id)
+
+
+class BibliographicalEntryNotFound(EntryNotFoundError):
pass
@@ -182,30 +190,83 @@ 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
+ try:
+ resp = uniprot_client.retrieve(uniprot_id)
+ except TypeError:
+ raise EntryNotFoundError(uniprot_id)
+ if resp.root=='':
+ raise EntryNotFoundError(uniprot_id)
+ try:
+ recommended_name = resp.root.findall(
+ 'u:entry/u:protein/u:recommendedName/u:fullName', ns)[0].text
+ except:
+ recommended_name = None
+ try:
+ recommended_short_name = resp.root.findall(
+ 'u:entry/u:protein/u:recommendedName/u:shortName', ns)[0].text
+ except:
+ recommended_short_name = None
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
+ gene_names = []
+ for el in resp.root.findall('u:entry/u:gene/u:name', ns):
+ gene_name = {'name':el.text, 'type':el.attrib['type']}
+ gene_names.append(gene_name)
+ try:
+ gene_id = resp.root.findall(
+ 'u:entry/u:dbReference[@type="GeneID"]', ns)[0].attrib['id']
+ except IndexError:
+ gene_id = None
entry_name = resp.root.findall('u:entry/u:name', ns)[0].text
go_els = resp.root.findall('u:entry/u:dbReference[@type="GO"]', ns)
+ accessions = [el.text for el in resp.root.findall('u:entry/u:accession', ns)]
molecular_functions = []
+ cellular_localisations = []
+ biological_processes = []
for go_el in go_els:
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:])
+ if term_property_value[0:2] == 'C:':
+ cellular_localisations.append('GO_' + go_el.attrib['id'][3:])
+ if term_property_value[0:2] == 'P:':
+ biological_processes.append('GO_' + go_el.attrib['id'][3:])
+ citations = []
+ for el in resp.root.findall('u:entry/u:reference', ns):
+ try:
+ doi = el.findall('u:citation/u:dbReference[@type="DOI"]', ns)[0].attrib['id']
+ pmid = el.findall('u:citation/u:dbReference[@type="PubMed"]', ns)[0].attrib['id']
+ citations.append({'doi':doi, 'pmid':pmid})
+ except IndexError:
+ continue
+ alternative_names = []
+ for el in resp.root.findall('u:entry/u:protein/u:alternativeName', ns):
+ alternative_name = {'full':el.findall('u:fullName',ns)[0].text}
+ if el.findall('u:shortName', ns):
+ alternative_name['short'] = el.findall('u:shortName', ns)[0].text
+ alternative_names.append(alternative_name)
+
+ db_references = resp.root.findall('u:entry/u:dbReference[@type="Pfam"]', ns)
+ domains = []
+ for db_reference in db_references:
+ name = db_reference.attrib["id"]
+ domains.append(name)
+
return {'recommended_name': recommended_name,
+ 'recommended_short_name': recommended_short_name,
'organism': int(organism),
- 'gene': gene,
+ 'gene_id': int(gene_id) if gene_id else None,
+ 'accessions': accessions,
+ 'gene_names': gene_names,
'entry_name': entry_name,
'short_name': entry_name.split('_')[0],
- 'molecular_functions': molecular_functions
+ 'molecular_functions': molecular_functions,
+ 'domains': domains,
+ 'cellular_localisations': cellular_localisations,
+ 'biological_processes': biological_processes,
+ 'citations': citations,
+ 'alternative_names': alternative_names
}
@@ -272,6 +333,8 @@ def get_pdb_uniprot_mapping(pdb_id):
pdb_id = pdb_id.lower()
resp = requests.get(
'https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{}'.format(pdb_id.lower()))
+ if resp.status_code != 200:
+ raise EntryNotFoundError(pdb_id)
uniprot_ids = list(resp.json()[pdb_id]['UniProt'].keys())
return uniprot_ids