def test_finding_end_gene(self):
inputs = {
"STAUR_3972": ['PKS_KR'],
"STAUR_3982":
['PKS_KS', 'PKS_AT', 'PKS_DH2', 'PKS_KR', 'ACP', 'Thioesterase'],
"STAUR_3983": ['PKS_KS', 'PKS_AT', 'PKS_DH', 'PKS_KR', 'ACP'],
"STAUR_3984": ['PKS_KS', 'PKS_AT', 'PKS_DH', 'PKS_KR', 'ACP']
}
genes = {}
for name, domains in inputs.items():
cds = DummyCDS(locus_tag=name)
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domains
genes[name] = cds
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert end.get_name() == "STAUR_3982"
genes["STAUR_3983"].nrps_pks.domain_names.append("TD")
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert not end
genes["STAUR_3984"].nrps_pks.domain_names.append("Thiosterase")
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert not end
def test_finding_start_gene(self):
inputs = {"STAUR_3972": ['PKS_KR'],
"STAUR_3983": ['PKS_KS', 'PKS_AT', 'PKS_DH', 'PKS_KR', 'ACP'],
"STAUR_3984": ['PKS_KS', 'PKS_AT', 'PKS_DH', 'PKS_KR', 'ACP'],
"STAUR_3985": ['ACP', 'PKS_KS', 'PKS_AT', 'PKS_DH', 'PKS_KR', 'ACP']}
genes = {}
for name, domains in inputs.items():
cds = DummyCDS(locus_tag=name)
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domains
genes[name] = cds
# no starts
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert not end
# fallback start
genes["STAUR_3983"].nrps_pks.domain_names = ["PKS_KS", "PKS_AT", "ACP"]
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert start.get_name() == "STAUR_3983"
assert not end
# two fallback start possibilities
genes["STAUR_3984"].nrps_pks.domain_names = ["PKS_KS", "PKS_AT", "ACP"]
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert not end
# first-class start
genes["STAUR_3972"].nrps_pks.domain_names = ["PKS_AT", "ACP"]
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert start.get_name() == "STAUR_3972"
assert not end
# two possible starts
genes["STAUR_3984"].nrps_pks.domain_names = ["PKS_AT", "ACP"]
start, end = orderfinder.find_first_and_last_cds(genes.values())
assert not start
assert not end
