def add_to_record(self, record: Record) -> None:
db_version = pfamdb.get_db_version_from_path(self.database)
for i, hit in enumerate(self.hits):
pfam_feature = PFAMDomain(FeatureLocation(hit["start"], hit["end"],
hit["strand"]),
description=hit["description"])
for key in [
"label", "locus_tag", "domain", "evalue", "score",
"translation", "db_xref"
]:
setattr(pfam_feature, key, hit[key])
pfam_feature.tool = self.tool
pfam_feature.database = db_version
pfam_feature.detection = "hmmscan"
pfam_feature.domain_id = "{}_{}_{:04d}".format(
self.tool, pfam_feature.locus_tag, i + 1)
record.add_pfam_domain(pfam_feature)
def test_pfam_domain(self):
original = PFAMDomain(FeatureLocation(2, 5), description="test",
protein_start=5, protein_end=10,
domain="p450")
original.db_xref.append("test-ref")
original.tool = "toolname"
original.domain_id = "domain_id"
original.database = "db"
original.detection = "someprogram"
original.evalue = 1e-5
original.score = 5.
original.locus_tag = "locus"
original.label = "somelabel"
original.translation = "ARNDCQ"
original.gene_ontologies = GOQualifier({'GO:0004871': 'signal transducer activity',
'GO:0007165': 'signal transduction',
'GO:0016020': 'membrane'})
new = PFAMDomain.from_biopython(original.to_biopython()[0])
for slot in ["db_xref", "tool", "domain_id", "database", "detection",
"evalue", "score", "locus_tag", "label", "translation", "domain",
"protein_start", "protein_end"]:
assert getattr(original, slot) == getattr(new, slot)
assert original.gene_ontologies.go_entries == new.gene_ontologies.go_entries