def get_gos_for_pfams(
record: Record) -> Dict[PFAMDomain, List[GeneOntologies]]:
""" Find Gene Ontology terms for a record's Pfam domains.
Arguments:
record: Record instance to annotate with Gene Ontology information
Returns:
A dictionary mapping a specific PFAMDomain instance to a list of GeneOntologies within the PFAMDomain.
"""
pfam_domains_with_gos = defaultdict(
list) # type: Dict[PFAMDomain, List[GeneOntologies]]
pfams = record.get_pfam_domains()
full_gomap_as_ontologies = construct_mapping(
path.get_full_path(__file__, 'data', 'pfam2go-march-2018.txt'))
if not pfams:
logging.debug(
'No Pfam domains found in record, cannot create Pfam to Gene Ontology mapping'
)
for pfam in pfams:
pfam_ids = pfam.db_xref
if not pfam_ids:
logging.debug(
'No Pfam ids found in Pfam domain %s, cannot create Pfam to Gene Ontology mapping',
pfam)
for pfam_id in pfam_ids:
pfam_id = pfam_id.partition('.')[0] # strip out version number
if not (len(pfam_id) == 7 and pfam_id[:2] == 'PF'
and pfam_id[2:].isdecimal()):
raise ValueError(
'Pfam id {} is not a valid Pfam id'.format(pfam_id))
gene_ontologies_for_pfam = full_gomap_as_ontologies.get(pfam_id)
if gene_ontologies_for_pfam:
pfam_domains_with_gos[pfam].append(gene_ontologies_for_pfam)
return pfam_domains_with_gos
def from_json(json: Dict[str, Any],
record: Record) -> Optional["Pfam2GoResults"]:
""" Constructs a new Pfam2GoResults instance from a json format and the
original record analysed.
Arguments:
json: JSON representation of Pfam2GoResults
record: Record analysed
Returns:
A Pfam2GoResults instance constructed from the record and the JSON
"""
if json["schema_version"] != Pfam2GoResults.schema_version:
logging.warning(
"Schema version mismatch, discarding Pfam2GO results")
return None
all_pfam_ids_to_ontologies = defaultdict(
list) # type: Dict[PFAMDomain, List[GeneOntologies]]
for domain in record.get_pfam_domains():
for pfam_id in domain.db_xref:
id_without_version = pfam_id.partition('.')[0]
if id_without_version in json["pfams"]:
all_ontology = [
GeneOntology(go_id, go_description)
for go_id, go_description in json["pfams"]
[id_without_version].items()
]
all_pfam_ids_to_ontologies[domain].append(
GeneOntologies(id_without_version, all_ontology))
results = Pfam2GoResults(record.id, all_pfam_ids_to_ontologies)
return results
def get_gos_for_pfams(
record: Record) -> Dict[PFAMDomain, List[GeneOntologies]]:
""" Find Gene Ontology terms for a record's Pfam domains.
Arguments:
record: Record instance to annotate with Gene Ontology information
Returns:
A dictionary mapping a specific PFAMDomain instance to a list of GeneOntologies within the PFAMDomain.
"""
pfam_domains_with_gos = defaultdict(
list) # type: Dict[PFAMDomain, List[GeneOntologies]]
pfams = record.get_pfam_domains()
full_gomap_as_ontologies = construct_mapping(
path.get_full_path(__file__, 'data', 'pfam2go-march-2018.txt'))
if not pfams:
logging.debug(
'No Pfam domains found in record, cannot create Pfam to Gene Ontology mapping'
)
for pfam in pfams:
gene_ontologies_for_pfam = full_gomap_as_ontologies.get(
pfam.identifier)
if gene_ontologies_for_pfam:
pfam_domains_with_gos[pfam].append(gene_ontologies_for_pfam)
return pfam_domains_with_gos
