def setUp(self):
self.genes = []
self.regions = []
domain_names = self.gen_domain_names()
for product in ['not_atpks', 'transatpks']:
cluster = helpers.DummyProtocluster(1, 2, product=product)
candidate_cluster = helpers.DummyCandidateCluster([cluster])
self.regions.append(Region(candidate_clusters=[candidate_cluster]))
for i in range(7):
locus_tag = chr(ord('a') + i)
if i == 6:
locus_tag = "all"
cds = helpers.DummyCDS(1, 2, locus_tag=locus_tag)
cds.product = product
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domain_names["nrpspksdomains_" +
locus_tag]
cds.cluster = cluster
cluster.add_cds(cds)
self.genes.append(cds)
self.regions[-1].add_cds(cds)
assert cds.region == self.regions[-1]
self.predictions = [
'redmxmal', 'ccmal', 'ohemal', 'ohmxmal', 'ohmmal', 'ccmmal',
'emal', 'redmmal', 'mmal', 'ccmxmal', 'mxmal', 'redemal', 'ohmal',
'mal', 'ccemal'
]
def setUp(self):
self.index = 0
self.old_blast_inputs = core.create_blast_inputs
core.create_blast_inputs = self.dummy_blast_inputs
self.dummy_cluster = DummyCluster(1, 100)
self.supercluster = DummySuperCluster([self.dummy_cluster])
self.region = Region([self.supercluster], [])
self.regions = [self.region, self.region]