def build_hits(record: Record, hmmscan_results: List, min_score: float,
max_evalue: float, database: str) -> List[Dict[str, Any]]:
""" Builds PFAMDomains from the given hmmscan results
Arguments:
record: the Record being scanned
hmmscan_results: the results of Bio.SearchIO.parse
min_score: a minimum allowable bitscore for hits (exclusive)
max_evalue: a maximum allowable evalue for hits (exclusive)
database: the name of the database used to find the hits
Returns:
a list of JSON representations of hmmer hits
"""
logging.debug("Generating feature objects for PFAM hits")
hits = []
feature_by_id = record.get_cds_name_mapping()
for result in hmmscan_results:
for hsp in result.hsps:
if hsp.bitscore <= min_score or hsp.evalue >= max_evalue:
continue
feature = feature_by_id[hsp.query_id]
location = feature.get_sub_location_from_protein_coordinates(hsp.query_start, hsp.query_end)
hit = {"location": str(location),
"label": result.id, "locus_tag": feature.get_name(),
"domain": hsp.hit_id, "evalue": hsp.evalue, "score": hsp.bitscore,
"translation": feature.translation[hsp.query_start:hsp.query_end + 1],
"identifier": pfamdb.get_pfam_id_from_name(hsp.hit_id, database),
"description": hsp.hit_description, "protein_start": hsp.query_start, "protein_end": hsp.query_end}
hits.append(hit)
return hits
def build_hits(record, hmmscan_results, min_score: float, max_evalue: float,
database: str) -> List[Dict[str, Any]]:
"Builds PFAMDomains from the given hmmscan results"
logging.debug("Generating feature objects for PFAM hits")
hits = []
feature_by_id = record.get_cds_name_mapping()
for result in hmmscan_results:
for hsp in result.hsps:
if hsp.bitscore <= min_score or hsp.evalue >= max_evalue:
continue
if hsp.query_id not in hsp.query_id:
continue
feature = feature_by_id[hsp.query_id]
start, end = calculate_start_and_end(feature, hsp)
dummy_feature = PFAMDomain(FeatureLocation(
start, end, feature.location.strand),
description="")
hit = {
"start":
start,
"end":
end,
"strand":
feature.location.strand,
"label":
result.id,
"locus_tag":
feature.locus_tag,
"domain":
hsp.hit_id,
"evalue":
hsp.evalue,
"score":
hsp.bitscore,
"translation":
str(
dummy_feature.extract(
record.seq).translate(table=feature.transl_table)),
"db_xref":
[pfamdb.get_pfam_id_from_name(hsp.hit_id, database)],
"description":
hsp.hit_description
}
hits.append(hit)
return hits