def test_compound_in_simple(self):
simple = FeatureLocation(10, 40)
compound = build_compound([(10, 20), (20, 40)], strand=1)
assert location_contains_other(simple, compound)
compound = build_compound([(10, 20), (20, 40), (50, 60)], strand=1)
assert not location_contains_other(simple, compound)
def is_contained_by(self, other: Union["Feature", Location]) -> bool:
""" Returns True if the given feature is wholly contained by this
feature.
"""
if isinstance(other, Feature):
return location_contains_other(other.location, self.location)
if isinstance(other, (CompoundLocation, FeatureLocation)):
return location_contains_other(other, self.location)
raise TypeError("Container must be a Feature, CompoundLocation or FeatureLocation, not %s" % type(other))
def test_simple_in_compound(self):
simple = FeatureLocation(5, 10)
compound = build_compound([(1, 4), (12, 20)], strand=1)
assert not location_contains_other(compound, simple)
simple = FeatureLocation(1, 20)
assert not location_contains_other(compound, simple)
simple = FeatureLocation(15, 18)
assert location_contains_other(compound, simple)
for part in compound.parts:
assert location_contains_other(compound, part)
def remove_redundant_protoclusters(
clusters: List[Protocluster],
rules_by_name: Dict[str,
rule_parser.DetectionRule]) -> List[Protocluster]:
""" Removes clusters which have superiors covering the same (or larger) region
"""
clusters_by_rule = defaultdict(list) # type: Dict[str, List[Protocluster]]
for cluster in clusters:
clusters_by_rule[cluster.product].append(cluster)
trimmed_clusters = []
for cluster in clusters:
rule_name = cluster.product
is_redundant = False
for superior in rules_by_name[rule_name].superiors:
for other_cluster in clusters_by_rule.get(superior, []):
if location_contains_other(other_cluster.core_location,
cluster.core_location):
is_redundant = True
break
if is_redundant:
break
if not is_redundant:
trimmed_clusters.append(cluster)
return trimmed_clusters
def test_simple_in_simple(self):
inner = FeatureLocation(5, 10)
outer = FeatureLocation(1, 20)
# clear contains
assert location_contains_other(outer, inner)
assert not location_contains_other(inner, outer)
# on one edge
outer = FeatureLocation(5, 20)
assert location_contains_other(outer, inner)
assert not location_contains_other(inner, outer)
# on both edges
outer = FeatureLocation(1, 20)
assert location_contains_other(outer, inner)
assert not location_contains_other(inner, outer)