def create_cluster(n_start, start, end, n_end, product='a'):
cluster = Protocluster(FeatureLocation(start, end),
FeatureLocation(n_start, n_end),
tool="testing",
product=product,
cutoff=1,
neighbourhood_range=0,
detection_rule="some rule text")
cds = create_cds(start, end, [product])
cluster.add_cds(cds)
return cluster
def create_cluster(self, rule_name, start, end):
rule = self.rules_by_name[rule_name]
core = FeatureLocation(start, end)
surrounds = FeatureLocation(max(0, start - rule.neighbourhood), end + rule.neighbourhood)
return Protocluster(core, surrounds, tool="testing", cutoff=rule.cutoff,
neighbourhood_range=rule.neighbourhood, product=rule_name,
detection_rule="rule text")
def create_cluster():
cluster = Protocluster(FeatureLocation(8, 71, strand=1),
FeatureLocation(3, 76, strand=1),
tool="test",
cutoff=17,
neighbourhood_range=5,
product='a',
detection_rule="some rule text")
return cluster
def test_product(self):
loc = FeatureLocation(1, 6, strand=1)
for bad in [
"-", "-like", "NRPS-", "NRPS PKS", "NRPS/PKS", "NRPS,PKS",
"NRPS.PKS"
]:
with self.assertRaisesRegex(ValueError,
"invalid protocluster product"):
Protocluster(loc,
loc,
tool="test",
cutoff=17,
neighbourhood_range=5,
product=bad,
detection_rule="some rule text")
def test_biopython_conversion(self):
bio = self.cluster.to_biopython()
assert len(bio) == 2
assert bio[0].type == "protocluster" and bio[1].type == "proto_core"
new = Protocluster.from_biopython(bio[0])
assert new is not self.cluster
assert new.cutoff == self.cluster.cutoff == 17
assert new.neighbourhood_range == self.cluster.neighbourhood_range == 5
assert new.product == self.cluster.product == 'a'
assert new.location.start == self.cluster.location.start == 3
assert new.core_location.start == self.cluster.core_location.start == 8
assert new.detection_rule == self.cluster.detection_rule == "some rule text"
assert new.tool == self.cluster.tool == "test"
assert new.location.start == self.cluster.location.start == 3
assert new.location.end == self.cluster.location.end == 76
assert new.core_location.start == self.cluster.core_location.start == 8
assert new.core_location.end == self.cluster.core_location.end == 71