def fix_disease_id(self, evidence, logger=logging.getLogger(__name__)):
disease_id = evidence['disease']['id']
new_disease_id = get_ontology_code_from_url(disease_id)
if len(new_disease_id.split('_')) != 2:
self.logger.warning("could not recognize disease.id: %s | added anyway" % disease_id)
evidence['disease']['id'] = new_disease_id
if not new_disease_id:
self.logger.warning("No valid disease.id could be found in evidence: %s. Offending disease.id: %s" % (
evidence['id'], disease_id))
def get_extended_evidence(self, evidence):
extended_evidence = copy.copy(evidence.evidence)
extended_evidence['private'] = dict()
# Get generic gene info
genes_info = []
pathway_data = dict(pathway_type_code=[],
pathway_code=[])
GO_terms = dict(biological_process=[],
cellular_component=[],
molecular_function=[],
)
target_class = dict(level1=[],
level2=[])
uniprot_keywords = []
# TODO: handle domains
geneid = extended_evidence['target']['id']
# try:
gene = self._get_gene_obj(geneid)
genes_info = ExtendedInfoGene(gene)
if 'facets' in gene._private and 'reactome' in gene._private['facets']:
pathway_data['pathway_type_code'].extend(gene._private['facets']['reactome']['pathway_type_code'])
pathway_data['pathway_code'].extend(gene._private['facets']['reactome']['pathway_code'])
# except Exception:
# self.logger.warning("Cannot get generic info for gene: %s" % aboutid)
if gene.go:
for go in gene.go:
go_code, data = go['id'], go['value']
try:
category, term = data['term'][0], data['term'][2:]
if category == 'P':
GO_terms['biological_process'].append(dict(code=go_code,
term=term))
elif category == 'F':
GO_terms['molecular_function'].append(dict(code=go_code,
term=term))
elif category == 'C':
GO_terms['cellular_component'].append(dict(code=go_code,
term=term))
except:
pass
if gene.uniprot_keywords:
uniprot_keywords = gene.uniprot_keywords
if genes_info:
extended_evidence["target"][ExtendedInfoGene.root] = genes_info.data
if pathway_data['pathway_code']:
pathway_data['pathway_type_code'] = list(set(pathway_data['pathway_type_code']))
pathway_data['pathway_code'] = list(set(pathway_data['pathway_code']))
if 'chembl' in gene.protein_classification and gene.protein_classification['chembl']:
target_class['level1'].append([i['l1'] for i in gene.protein_classification['chembl'] if 'l1' in i])
target_class['level2'].append([i['l2'] for i in gene.protein_classification['chembl'] if 'l2' in i])
# Get generic efo info
# can it happen you get no efo codes but just one disease?
all_efo_codes = []
diseaseid = extended_evidence['disease']['id']
efo = self._get_efo_obj(diseaseid)
efo_info = ExtendedInfoEFO(efo)
if efo_info:
for path in efo_info.data['path']:
all_efo_codes.extend(path)
extended_evidence["disease"][ExtendedInfoEFO.root] = efo_info.data
all_efo_codes = list(set(all_efo_codes))
# Get generic eco info
try:
all_eco_codes = extended_evidence['evidence']['evidence_codes']
try:
all_eco_codes.append(
get_ontology_code_from_url(extended_evidence['evidence']['gene2variant']['functional_consequence']))
except KeyError:
pass
ecos_info = []
for eco_id in all_eco_codes:
eco = self._get_eco_obj(eco_id)
if eco is not None:
ecos_info.append(ExtendedInfoECO(eco))
else:
self.logger.warning("eco uri %s is not in the ECO LUT so it will not be considered as included", eco_id)
if ecos_info:
data = []
for eco_info in ecos_info:
data.append(eco_info.data)
extended_evidence['evidence'][ExtendedInfoECO.root] = data
except Exception as e:
extended_evidence['evidence'][ExtendedInfoECO.root] = None
all_eco_codes = []
# self.logger.exception("Cannot get generic info for eco: %s:"%str(e))
# Add private objects used just for faceting
extended_evidence['private']['efo_codes'] = all_efo_codes
extended_evidence['private']['eco_codes'] = all_eco_codes
extended_evidence['private']['datasource'] = evidence.datasource
extended_evidence['private']['datatype'] = evidence.datatype
extended_evidence['private']['facets'] = {}
if pathway_data['pathway_code']:
extended_evidence['private']['facets']['reactome'] = pathway_data
if uniprot_keywords:
extended_evidence['private']['facets']['uniprot_keywords'] = uniprot_keywords
if GO_terms['biological_process'] or \
GO_terms['molecular_function'] or \
GO_terms['cellular_component']:
extended_evidence['private']['facets']['go'] = GO_terms
if target_class['level1']:
extended_evidence['private']['facets']['target_class'] = target_class
return Evidence(extended_evidence, self.datasources_to_datatypes)
def fix_evidence(self, evidence):
evidence = evidence.evidence
fixed = False
# fix errors in data here so nobody needs to ask corrections to the data provider
# fix missing version in gwas catalog data
if 'variant2disease' in evidence:
try:
float(evidence['evidence']['variant2disease']['provenance_type']['database']['version'])
except:
evidence['evidence']['variant2disease']['provenance_type']['database']['version'] = ''
fixed = True
try:
float(evidence['evidence']['variant2disease']['provenance_type']['database']['dbxref']['version'])
except:
evidence['evidence']['variant2disease']['provenance_type']['database']['dbxref']['version'] = ''
fixed = True
if 'gene2variant' in evidence:
try:
float(evidence['evidence']['gene2variant']['provenance_type']['database']['version'])
except:
evidence['evidence']['gene2variant']['provenance_type']['database']['version'] = ''
fixed = True
try:
float(evidence['evidence']['gene2variant']['provenance_type']['database']['dbxref']['version'])
except:
evidence['evidence']['gene2variant']['provenance_type']['database']['dbxref']['version'] = ''
fixed = True
# Split EVA in two datasources depending on the datatype
if (evidence['sourceID'] == 'eva') and \
(evidence['type'] == 'somatic_mutation'):
evidence['sourceID'] = 'eva_somatic'
fixed = True
# Move genetic_literature to genetic_association
if evidence['type'] == 'genetic_literature':
evidence['type'] = 'genetic_association'
if 'provenance_type' in evidence and \
'database' in evidence['provenance_type'] and \
'version' in evidence['provenance_type']['database']:
evidence['provenance_type']['database']['version'] = str(evidence['provenance_type']['database']['version'])
# Enforce eco-based score for genetic_association evidencestrings
if evidence['type'] == 'genetic_association':
available_score = None
eco_uri = None
try:
available_score = evidence['evidence']['gene2variant']['resource_score']['value']
except KeyError:
if 'resource_score' in evidence['evidence'] and \
'value' in evidence['evidence']['resource_score']:
available_score = evidence['evidence']['resource_score']['value']
try:
eco_uri = evidence['evidence']['gene2variant']['functional_consequence']
if 'evidence_codes' in evidence['evidence']:
eco_uri = evidence['evidence']['evidence_codes']
except KeyError:
if 'evidence_codes' in evidence['evidence']:
eco_uri = evidence['evidence']['evidence_codes'][0]
eco_uri.rstrip()
if eco_uri in self.eco_scores:
if 'gene2variant' in evidence['evidence']:
if 'resource_score' not in evidence['evidence']['gene2variant']:
evidence['evidence']['gene2variant']['resource_score'] = {}
evidence['evidence']['gene2variant']['resource_score']['value'] = self.eco_scores[eco_uri]
evidence['evidence']['gene2variant']['resource_score']['type'] = 'probability'
if available_score != self.eco_scores[eco_uri]:
fixed = True
else:
self.logger.warning("Cannot find a score for eco code %s in evidence id %s" % (eco_uri, evidence['id']))
# Remove identifiers.org from genes and map to ensembl ids
self.fix_target_id(evidence, self.available_genes, self.non_reference_genes )
# Remove identifiers.org from cttv activity and target type ids
if 'target_type' in evidence['target']:
evidence['target']['target_type'] = evidence['target']['target_type'].split('/')[-1]
if 'activity' in evidence['target']:
evidence['target']['activity'] = evidence['target']['activity'].split('/')[-1]
# Remove identifiers.org from efos
self.fix_disease_id(evidence)
# Remove identifiers.org from ecos
new_eco_ids = []
if 'evidence_codes' in evidence['evidence']:
eco_ids = evidence['evidence']['evidence_codes']
elif 'variant2disease' in evidence['evidence']:
if 'variant2disease' in evidence['evidence']:
eco_ids = evidence['evidence']['variant2disease']['evidence_codes']
if 'gene2variant' in evidence['evidence']:
eco_ids.extend(evidence['evidence']['gene2variant']['evidence_codes'])
elif 'target2drug' in evidence['evidence']:
eco_ids = evidence['evidence']['target2drug']['evidence_codes']
eco_ids.extend(evidence['evidence']['drug2clinic']['evidence_codes'])
elif 'biological_model' in evidence['evidence']:
eco_ids = evidence['evidence']['biological_model']['evidence_codes']
else:
eco_ids = [] # something wrong here...
eco_ids = list(set(eco_ids))
for idorg_eco_uri in eco_ids:
code = get_ontology_code_from_url(idorg_eco_uri.strip())
if code is not None:
# if len(code.split('_')) != 2:
# self.logger.warning("could not recognize evidence code: %s in id %s | added anyway" %(evidence['id'],
# idorg_eco_uri))
new_eco_ids.append(code)
evidence['evidence']['evidence_codes'] = list(set(new_eco_ids))
if not new_eco_ids:
self.logger.warning("No valid ECO could be found in evidence: %s. original ECO mapping: %s" % (
evidence['id'], str(eco_ids)[:100]))
return Evidence(evidence,self.datasources_to_datatypes), fixed