def test_pfam_domain(self):
original = PFAMDomain(FeatureLocation(2, 5),
description="test",
protein_start=5,
protein_end=10,
identifier="PF00002.17",
domain="p450",
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 [
"tool", "domain_id", "database", "detection", "evalue",
"score", "locus_tag", "label", "translation", "domain",
"protein_start", "protein_end", "identifier", "version"
]:
assert getattr(original, slot) == getattr(new, slot)
assert original.gene_ontologies.go_entries == new.gene_ontologies.go_entries
assert original.full_identifier == new.full_identifier
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):
protein_location = FeatureLocation(hit["protein_start"], hit["protein_end"])
pfam_feature = PFAMDomain(location_from_string(hit["location"]),
description=hit["description"], protein_location=protein_location,
identifier=hit["identifier"], tool=self.tool, locus_tag=hit["locus_tag"])
for key in ["label", "locus_tag", "domain", "evalue",
"score", "translation"]:
setattr(pfam_feature, key, hit[key])
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 add_to_record(self, record: Record) -> None:
""" Adds the hits as PFAMDomains to the given record """
db_version = pfamdb.get_db_version_from_path(self.database)
for i, hit in enumerate(self.hits):
protein_location = FeatureLocation(hit.protein_start, hit.protein_end)
pfam_feature = PFAMDomain(location_from_string(hit.location),
description=hit.description, protein_location=protein_location,
identifier=hit.identifier, tool=self.tool, locus_tag=hit.locus_tag)
for key in ["label", "locus_tag", "domain", "evalue",
"score", "translation"]:
setattr(pfam_feature, key, getattr(hit, key))
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)