def test_too_many_in_circular(self, _patched_bridge):
features = [
SeqFeature(build_compound([(10, 30), (0, 9)], -1), type="CDS"),
SeqFeature(build_compound([(10, 30), (0, 9)], -1), type="gene"),
SeqFeature(build_compound([(10, 30), (0, 9)], -1), type="CDS")
]
with self.assertRaisesRegex(ValueError, "inconsistent exon ordering"):
self.check(features, circular=True)
def test_inconsistent(self):
features = [
SeqFeature(build_compound([(10, 30), (40, 70)], -1), type="CDS"),
SeqFeature(build_compound([(40, 70), (10, 30)], -1), type="gene"),
SeqFeature(build_compound([(40, 70), (10, 30)], None),
type="other")
]
with self.assertRaisesRegex(ValueError, "inconsistent exon ordering"):
self.check(features)
def test_reversed(self):
features = [
SeqFeature(build_compound([(10, 30), (40, 70)], -1), type="CDS"),
SeqFeature(build_compound([(10, 30), (40, 70)], -1), type="gene"),
SeqFeature(build_compound([(40, 70), (10, 30)], None),
type="other")
]
self.check(features)
for feature in features:
assert feature.location.parts[0].start == 40
def test_overlapping_exons(self, _patched_overlap):
features = [SeqFeature(FeatureLocation(5, 8, 1))]
with self.assertRaisesRegex(ValueError, "contains overlapping exons"):
self.check(features)
def test_outside_seq(self):
features = [SeqFeature(FeatureLocation(50, 140, 1))]
with self.assertRaisesRegex(ValueError,
"feature outside record sequence"):
self.check(features)