def chebi2name(self, name):
"""Return the ASCII name of a CHEBI identifier"""
from bioservices import ChEBI
c = ChEBI()
name = dict(c.getLiteEntity(name)[0])["chebiAsciiName"]
return name
def _lookup_chebi_id(self):
chebi_web = ChEBI()
lookup_id = str(self.external_id)
if not lookup_id.startswith("CHEBI:"):
lookup_id = "CHEBI:{}".format(self.external_id)
chebi = chebi_web.getCompleteEntity(lookup_id)
if not chebi:
self.error = "No results found when querying ChEBI for {}".format(
self.external_id)
return self
# Synonyms
# We get duplicates so filter these.
if self.get_synonyms:
try:
seen_it = {}
for item in chebi.Synonyms:
if item.data not in seen_it:
self.synonyms.append(item.data)
seen_it[item.data] = 1
except AttributeError:
pass # Some may not have synonyms apparently
# Name
self.name = chebi.chebiAsciiName
# inchikey
try:
self.inchikey = chebi.inchiKey
except AttributeError:
self.error = 'No InChIKey found for entry: {}'.format(
self.external_id)
return self
def test_completelist():
ch = ChEBI()
names = [
x.chebiAsciiName
for x in ch.getCompleteEntityByList(["CHEBI:27732", "CHEBI:36707"])
]
assert names == [
"caffeine", "2-acetyl-1-alkyl-sn-glycero-3-phosphocholine"
]
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
res = ch.getLiteEntity("194.19076", "MASS", 5, 2)
assert res[0]["chebiId"] == "CHEBI:27732"
# should return nothing
res = ch.getLiteEntity("194.19076", "SMILES", 5, 2)
def get_single_compound_metadata_online(compound_id):
if compound_id.upper().startswith('C'):
s = KEGG()
res = s.get(compound_id)
return s.parse(res)
else:
ch = ChEBI()
res = ch.getCompleteEntity('CHEBI:'+compound_id)
return res
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
res = ch.getLiteEntity("194.19076", "MASS", 5, 2)
assert res[0]["chebiId"] == "CHEBI:27732"
# should return nothing
res = ch.getLiteEntity("194.19076", "SMILES", 5, 2)
def test_polymer():
ch = ChEBI()
x = ch.serv.getUpdatedPolymer("CHEBI:27732")
x.chebiId
#Out[14]: 27732
x.globalCharge
#0
x.globalFormula
# C8H10N4O2
x.updatedStructure
def kegg_to_chebi(compound_ids):
results = {}
ch = ChEBI()
for compound_id in compound_ids:
try:
if compound_id.startswith('C'):
res = ch.getLiteEntity(compound_id)
assert len(res) > 0 # we should always be able to convert from KEGG -> ChEBI ids
le = res[0]
chebi_number = le.chebiId.split(':')[1]
print('KEGG %s --> ChEBI %s' % (compound_id, chebi_number))
results[compound_id] = chebi_number
else:
print('ChEBI %s --> ChEBI %s' % (compound_id, compound_id))
results[compound_id] = compound_id
except Exception:
print('KEGG %s --> KEGG %s' % (compound_id, compound_id))
results[compound_id] = compound_id
return results
def get_compound_id(smiles):
""" returns kegg id for compund with given smiles """
indigo = Indigo()
# convert smiles to standard format
mol = indigo.loadMolecule(smiles)
mol.aromatize()
moi_smiles = mol.canonicalSmiles()
# Get list of possible kegg IDs
url = "http://rest.genome.jp/subcomp/?smiles=%s&cutoff=1.0" % smiles
http_client = HTTPClient()
try:
response = http_client.fetch(url).body
except HTTPError as e:
raise RuntimeError("Error:", str(e))
http_client.close()
subcomp_results = response.split("\n")
subcomp_results.pop()
subcomp_results = ([i.split('\t')[0] for i in subcomp_results])
# get smiles for all compound IDs found
all_smiles = []
uni = UniChem()
mapping = uni.get_mapping("kegg_ligand", "chebi")
ch = ChEBI()
all_smiles = [ch.getCompleteEntity(mapping[x]).smiles
for x in subcomp_results]
# convert smiles to a standard format
for pos, mol in enumerate(all_smiles):
m = indigo.loadMolecule(mol)
m.aromatize()
all_smiles[pos] = m.canonicalSmiles()
# check if smiles matches given and, if so, use that compound ID
# if not, errors out
try:
index = all_smiles.index(moi_smiles)
except:
raise RuntimeError("SMILES unmatchable to: %s" % str(all_smiles))
return subcomp_results[index]
'''
import os
import click
import json
import requests
import time
import xmltodict
import bioservices
from bioservices import KEGG, ChEBI
from zeep import Client
from tqdm import tqdm
k = KEGG(verbose=False)
map_kegg_chebi = k.conv("chebi", "compound")
c = ChEBI(verbose=False)
chebi_client = Client(
"https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl")
chemspider_client = Client("https://www.chemspider.com/InChI.asmx?WSDL")
# For compounds that cant be found at all.
not_founds = []
# Need to create a global dictonary for these annotations, as I don't
# want to take the piss with the web services these wonderful people
# provide to us free of charge.
global CONVERTED_COMPOUNDS
CONVERTED_COMPOUNDS = {}
def chebi2name(self, name):
"""Return the ASCII name of a CHEBI identifier"""
from bioservices import ChEBI
c = ChEBI()
name = dict(c.getLiteEntity(name)[0])['chebiAsciiName']
return name
def test_structure():
ch = ChEBI()
smiles = ch.getCompleteEntity("CHEBI:27732").smiles
ch.getStructureSearch(smiles, "SMILES", "SIMILARITY", 3, 0.25)
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "ChEMBL COMPOUND")
assert res == ["521332"]
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
assert res == ['C07484']
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_ontology():
ch = ChEBI()
ch.getAllOntologyChildrenInPath("CHEBI:27732", "has part")
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
def test_completelist():
ch = ChEBI()
names = [x.chebiAsciiName for x in ch.getCompleteEntityByList(["CHEBI:27732","CHEBI:36707"])]
names = [str(x) for x in names]
assert names == ["caffeine", "2-acetyl-1-alkyl-sn-glycero-3-phosphocholine"]
def test_chebi_mass():
ch = ChEBI()
mass1 = ch.getCompleteEntity("CHEBI:27732").mass
assert float(mass1) == 194.19076
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "KEGG COMPOUND accession")
assert res == ['C07484']
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_chebi():
ch = ChEBI()
ch.getCompleteEntity("CHEBI:10102")
res = ch.conv("CHEBI:10102", "ChEMBL COMPOUND")
assert res == ["521332"]
try:
res = ch.conv("CHEBI:10102", "wrong db")
assert False
except:
assert True
ch.getOntologyChildren("CHEBI:27732")
ch.getOntologyParents("CHEBI:27732")
ch.getUpdatedPolymer("CHEBI:27732")
def test_ontology():
ch = ChEBI()
ch.getAllOntologyChildrenInPath("CHEBI:27732", "has part")
def test_structure():
ch = ChEBI()
smiles = ch.getCompleteEntity("CHEBI:27732").smiles
ch.getStructureSearch(smiles, "SMILES", "SIMILARITY", 3, 0.25)
