def test_blank_records(self):
blank_no_pfams = DummyRecord()
blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna))
fake_pfam = DummyPFAMDomain(identifier="PF00000")
blank_no_ids.add_pfam_domain(fake_pfam)
assert not pfam2go.get_gos_for_pfams(blank_no_pfams)
assert not pfam2go.get_gos_for_pfams(blank_no_ids)
def test_blank_records(self):
blank_no_pfams = DummyRecord()
blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna))
fake_pfam_location = FeatureLocation(0, 12)
fake_pfam = PFAMDomain(location=fake_pfam_location,
description='MCPsignal',
protein_start=0,
protein_end=5,
identifier="PF00000",
tool="test")
fake_pfam.domain_id = 'BLANK'
blank_no_ids.add_pfam_domain(fake_pfam)
assert not pfam2go.get_gos_for_pfams(blank_no_pfams)
assert not pfam2go.get_gos_for_pfams(blank_no_ids)
def test_blank_records(self):
blank_no_pfams = DummyRecord()
blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna))
fake_pfam_location = FeatureLocation(0, 12)
fake_pfam = PFAMDomain(location=fake_pfam_location,
description='MCPsignal',
protein_start=0,
protein_end=5)
fake_pfam.domain_id = 'BLANK'
blank_no_ids.add_pfam_domain(fake_pfam)
with self.assertLogs(level='DEBUG') as log_cm:
gos_for_no_pfams = pfam2go.get_gos_for_pfams(blank_no_pfams)
assert 'No Pfam domains found' in str(log_cm.output)
assert not gos_for_no_pfams
gos_for_no_ids = pfam2go.get_gos_for_pfams(blank_no_ids)
assert 'No Pfam ids found' in str(log_cm.output)
assert not gos_for_no_ids
