def matchSpeciesChebi(s1, s2, logging=False):
""" Match two Chebi identifiers.
If matching returns the chebi information of the identifier.
:param s1: first chebi id
:type s1: str
:param s2: second chebi id
:type s2: str
:param logging: log messages to console
:type logging: bool
:return: dictionary of chebi information, returns None if no match
:rtype: dict
"""
ch = bioservices.ChEBI()
ch1 = getChebiId(s1)
ch2 = getChebiId(s2)
if not ch1 or not ch2:
return None
if logging:
print('Comparing %s (%s) with %s (%s)' %
(s1.getId(), ch1, s2.getId(), ch2))
try:
entry = ch.getCompleteEntity(ch1)
exact = []
if ch1 == ch2:
exact.append({'id': s2.getId()})
children = []
if hasattr(entry, 'OntologyChildren'):
for child in entry.OntologyChildren:
if child['chebiId'] == ch2:
children.append({'id': s2.getId(), 'data': child})
parents = []
if (hasattr(entry, 'OntologyParents')):
for parent in entry.OntologyParents:
if parent['chebiId'] == ch2:
parents.append({'id': s2.getId(), 'data': parent})
return {
'id': s1.getId(),
'chebi_name': entry.chebiAsciiName,
'exact': exact,
'children': children,
'parents': parents
}
except:
print("Unexpected error:", sys.exc_info()[0])
return None
def __init__(self, debug=False):
""" Creates and displays the search form. """
self.debug = debug
self.s = bioservices.BioModels()
self.ch = bioservices.ChEBI()
# Define widgets
# <Search>
self.wSearchTerm = w.Text(description='Search biomodels by species:',
value="CHEBI:17925")
self.wSearchTerm.on_submit(self.searchChebi)
self.wSearchButton = w.Button(description='Search')
self.wSearchButton.on_click(self.searchChebi)
self.wSearchChebi = w.HBox(
children=[self.wSearchTerm, self.wSearchButton])
self.wSelectChebis = w.Select(description='Matching ChEBI:',
width='600px',
height='250px')
# FIXME: update the deprecated functions
self.wSelectChebis.on_trait_change(self.selectChebi)
self.wSelectModels = w.Select(description='Matching BioModels:',
width='200px')
self.wSelectModels.on_trait_change(self.selectedModel)
# <Model>
self.wModelId = w.Text(description='Model ID:',
value="No model selected")
self.wModelCode = w.Text(description='Install Code:')
self.wModelImport = w.Text(description='Import module code:')
self.wModelSbml = w.Textarea(description='Model SBML:',
width='800px',
height='300px')
# <Container>
self.wModel = w.FlexBox(children=[
self.wModelId, self.wModelCode, self.wSelectModels,
self.wModelImport, self.wModelSbml
])
for ch in self.wModel.children:
ch.font_family = 'monospace'
ch.color = '#AAAAAA'
ch.background_color = 'black'
self.wContainer = w.FlexBox(
children=[self.wSearchChebi, self.wSelectChebis, self.wModel])
# display the widgets
display(self.wContainer)
# clear notebook output
clear_output()
def resolveAnnotationHelper(annotation):
if not hasattr(resolveAnnotation, "db"):
resolveAnnotation.db = {}
resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
resolveAnnotation.uni = bioservices.UniProt(verbose=False)
resolveAnnotation.k = bioservices.kegg.KEGG(verbose=False)
resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
resolveAnnotation.t = bioservices.Taxon()
resolveAnnotation.db[
"http://identifiers.org/uniprot/P62988"
] = "http://identifiers.org/uniprot/P62988"
resolveAnnotation.db[
"http://identifiers.org/uniprot/P06842"
] = "http://identifiers.org/uniprot/P06842"
resolveAnnotation.db[
"http://identifiers.org/uniprot/P07006"
] = "http://identifiers.org/uniprot/P06842"
if annotation in resolveAnnotation.db:
return annotation, resolveAnnotation.db[annotation]
tAnnotation = annotation.replace("%3A", ":")
tAnnotation = annotation.split("/")[-1]
# tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
try:
if "obo.go" in annotation or "/go/GO" in annotation:
res = resolveAnnotation.qg.Term(tAnnotation)
finalArray = []
if type(res) not in [int]:
res = bioservices.Service("name").easyXML(res)
tmp = res.findAll("name")
for x in tmp:
try:
tagString = str(goGrammar.parseString(str(x))[0])
if tagString not in ["Systematic synonym"]:
finalArray.append(str(goGrammar.parseString(str(x))[0]))
except pyp.ParseBaseException:
continue
if len(finalArray) > 0:
resolveAnnotation.db[annotation] = finalArray[0]
else:
resolveAnnotation.db[annotation] = ""
finalAnnotation = resolveAnnotation.db[annotation]
elif "kegg" in annotation:
data = resolveAnnotation.k.get(tAnnotation)
dict_data = resolveAnnotation.k.parse(data)
if type(dict_data) == int:
resolveAnnotation.db[annotation] = ""
else:
resolveAnnotation.db[annotation] = dict_data["name"]
finalAnnotation = resolveAnnotation.db[annotation]
elif "uniprot" in annotation:
identifier = annotation.split("/")[-1]
result = resolveAnnotation.uni.quick_search(identifier)
if identifier in result:
resolveAnnotation.db[annotation] = result[identifier][
"Protein names"
].split("(")[0]
else:
finalAnnotation = ""
finalAnnotation = resolveAnnotation.db[annotation]
elif "chebi" in annotation:
tmp = annotation.split("/")[-1]
entry = resolveAnnotation.ch.getLiteEntity(tmp)
finalAnnotation = ""
for element in entry:
resolveAnnotation.db[annotation] = str(element["chebiAsciiName"])
finalAnnotation = resolveAnnotation.db[annotation]
elif (
"cco" in annotation
or "pirsf" in annotation
or "pubchem" in annotation
or "omim" in annotation
):
finalAnnotation = ""
elif "taxonomy" in annotation:
# uniprot stuff for taxonomy
result = resolveAnnotation.t.search_by_taxon(tAnnotation)
resolveAnnotation.db[annotation] = result["Scientific Name"]
finalAnnotation = resolveAnnotation.db[annotation]
"""
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
"""
else:
return annotation, ""
# assert(False)
finalAnnotation = ""
except (IOError, KeyError) as e:
return annotation, ""
return annotation, finalAnnotation
def resolveAnnotationHelper(annotation):
if not hasattr(resolveAnnotation, 'db'):
resolveAnnotation.db = {}
resolveAnnotation.ch = bioservices.ChEBI(verbose=False)
resolveAnnotation.uni = bioservices.UniProt(verbose=False)
resolveAnnotation.k = bioservices.kegg.KEGG(verbose=False)
resolveAnnotation.qg = bioservices.QuickGO(verbose=False)
resolveAnnotation.t = bioservices.Taxon()
resolveAnnotation.db[
'http://identifiers.org/uniprot/P62988'] = 'http://identifiers.org/uniprot/P62988'
resolveAnnotation.db[
'http://identifiers.org/uniprot/P06842'] = 'http://identifiers.org/uniprot/P06842'
resolveAnnotation.db[
'http://identifiers.org/uniprot/P07006'] = 'http://identifiers.org/uniprot/P06842'
if annotation in resolveAnnotation.db:
return annotation, resolveAnnotation.db[annotation]
tAnnotation = annotation.replace('%3A', ':')
tAnnotation = annotation.split('/')[-1]
#tAnnotation = re.search(':([^:]+:[^:]+$)',tAnnotation).group(1)
try:
if 'obo.go' in annotation or '/go/GO' in annotation:
res = resolveAnnotation.qg.Term(tAnnotation)
finalArray = []
if type(res) not in [int]:
res = bioservices.Service('name').easyXML(res)
tmp = res.findAll('name')
for x in tmp:
try:
tagString = str(goGrammar.parseString(str(x))[0])
if tagString not in ['Systematic synonym']:
finalArray.append(
str(goGrammar.parseString(str(x))[0]))
except pyp.ParseBaseException:
continue
if len(finalArray) > 0:
resolveAnnotation.db[annotation] = finalArray[0]
else:
resolveAnnotation.db[annotation] = ''
finalAnnotation = resolveAnnotation.db[annotation]
elif 'kegg' in annotation:
data = resolveAnnotation.k.get(tAnnotation)
dict_data = resolveAnnotation.k.parse(data)
if type(dict_data) == int:
resolveAnnotation.db[annotation] = ''
else:
resolveAnnotation.db[annotation] = dict_data['name']
finalAnnotation = resolveAnnotation.db[annotation]
elif 'uniprot' in annotation:
identifier = annotation.split('/')[-1]
result = resolveAnnotation.uni.quick_search(identifier)
if identifier in result:
resolveAnnotation.db[annotation] = result[identifier][
'Protein names'].split('(')[0]
else:
finalAnnotation = ''
finalAnnotation = resolveAnnotation.db[annotation]
elif 'chebi' in annotation:
tmp = annotation.split('/')[-1]
entry = resolveAnnotation.ch.getLiteEntity(tmp)
finalAnnotation = ''
for element in entry:
resolveAnnotation.db[annotation] = str(
element['chebiAsciiName'])
finalAnnotation = resolveAnnotation.db[annotation]
elif 'cco' in annotation or 'pirsf' in annotation or 'pubchem' in annotation or 'omim' in annotation:
finalAnnotation = ''
elif 'taxonomy' in annotation:
#uniprot stuff for taxonomy
result = resolveAnnotation.t.search_by_taxon(tAnnotation)
resolveAnnotation.db[annotation] = result['Scientific Name']
finalAnnotation = resolveAnnotation.db[annotation]
'''
url = 'http://www.uniprot.org/taxonomy/'
params = {
'from':'ACC',
'to':'P_REFSEQ_AC',
'format':'tab',
'query':'P13368 P20806 Q9UM73 P97793 Q17192'
}
data = urllib.urlencode(params)
request = urllib2.Request(url, data)
contact = "" # Please set your email address here to help us debug in case of problems.
request.add_header('User-Agent', 'Python contact')
response = urllib2.urlopen(request)
page = response.read(200000)
'''
else:
return annotation, ''
#assert(False)
finalAnnotation = ''
except (IOError, KeyError) as e:
return annotation, ''
return annotation, finalAnnotation