def test_add_results_to_record(self):
pfams = {
'PF00015.2': FeatureLocation(0, 3),
'PF00351.1': FeatureLocation(0, 3),
'PF00015.27': FeatureLocation(3, 6)
}
fake_record = set_dummy_with_pfams(pfams)
fake_duplicate_pfam = PFAMDomain(location=FeatureLocation(6, 9),
description='DUPLICATE',
protein_start=0,
protein_end=5)
fake_duplicate_pfam.db_xref = ['PF00015.2']
fake_duplicate_pfam.domain_id = 'DUPLICATE'
fake_record.add_pfam_domain(fake_duplicate_pfam)
assert fake_duplicate_pfam in fake_record.get_pfam_domains()
gos_for_fake_pfam = pfam2go.get_gos_for_pfams(fake_record)
fake_results = pfam2go.Pfam2GoResults(fake_record.id,
gos_for_fake_pfam)
fake_results.add_to_record(fake_record)
assert fake_duplicate_pfam.db_xref == ['PF00015.2']
for pfam in fake_record.get_pfam_domains():
assert sorted(pfam.gene_ontologies.ids) == sorted(
fake_results.get_all_gos(pfam))
# make sure identical pfams (with different version numbers) all have the same gene ontologies
for pfam_id in pfam.db_xref:
if pfam_id.startswith('PF00015'):
assert sorted(pfam.gene_ontologies.ids) == sorted(
fake_results.get_all_gos(fake_duplicate_pfam))
def set_dummy_with_pfams(pfam_ids: Dict[str, FeatureLocation]) -> DummyRecord:
pfam_domains = []
for pfam_id, pfam_location in pfam_ids.items():
pfam_domain = PFAMDomain(location=pfam_location,
description='FAKE',
protein_start=0,
protein_end=5)
pfam_domain.db_xref = [pfam_id]
pfam_domain.domain_id = '%s.%d.%d' % (pfam_id, pfam_location.start,
pfam_location.end)
pfam_domains.append(pfam_domain)
return DummyRecord(features=pfam_domains)