def test_process_wgs_master_scaffolds_contig_with_seq(self):
"""Test process_wgs_master_scaffolds() doesn't get contigs if there is a CONTIG ann. but also a sequence"""
fake_records = [
FakeRecord(annotations={'contig': 'foo'}),
FakeRecord(annotations={'contig': 'bar'})
]
procesed = utils.process_wgs_master_scaffolds(fake_records)
self.assertEqual(fake_records, procesed)
def test_process_wgs_master_scaffolds_wgs_with_seq(self):
"""Test process_wgs_master_scaffolds() doesn't get contigs if there are WGS/WGS_SCAFLDs but also sequences"""
mock('utils.fix_wgs_master_record',
tracker=self.tt,
returns_func=lambda x: [x])
fake_records = [
FakeRecord(annotations={'wgs': 'foo'}),
FakeRecord(annotations={'wgs_scafld': 'bar'})
]
procesed = utils.process_wgs_master_scaffolds(fake_records)
self.assertEqual(fake_records, procesed)
def test_process_wgs_master_scaffolds_wgs(self):
"""Test process_wgs_master_scaffolds() gets contigs from NCBI if there are WGS/WGS_SCAFLD annotations"""
mock('utils.fix_wgs_master_record',
tracker=self.tt,
returns_func=lambda x: [x])
fake_records = [
FakeRecord(annotations={'wgs': 'foo'}),
FakeRecord(annotations={'wgs_scafld': 'bar'})
]
fake_records[0].seq = UnknownSeq(23)
fake_records[1].seq = UnknownSeq(42)
trace = """Called utils.fix_wgs_master_record(
<antismash.test.test_utils.FakeRecord object at ...>)
Called utils.fix_wgs_master_record(
<antismash.test.test_utils.FakeRecord object at ...>)
"""
procesed = utils.process_wgs_master_scaffolds(fake_records)
self.assertEqual(fake_records, procesed)
assert_same_trace(self.tt, trace)
def test_process_wgs_master_scaffolds_no_scaffolds(self):
"""Test process_wgs_master_scaffolds() does not change the list of records if there are no scaffolds"""
fake_records = [FakeRecord(), FakeRecord()]
procesed = utils.process_wgs_master_scaffolds(fake_records)
self.assertEqual(fake_records, procesed)