def test_conversion_with_codon_start_reverse(self):
seqf = SeqFeature(FeatureLocation(5, AfterPosition(12), -1))
seqf.type = "test"
for codon_start in "123":
seqf.qualifiers["codon_start"] = [codon_start]
feature = Feature.from_biopython(seqf)
assert feature._original_codon_start == int(codon_start) - 1
assert feature.location.end == AfterPosition(12 - feature._original_codon_start)
new = feature.to_biopython()[0]
assert new.qualifiers["codon_start"] == [codon_start]
assert new.location.start == seqf.location.start
assert new.location.end == seqf.location.end
def test_invalid_codon_start(self):
seqf = SeqFeature(FeatureLocation(5, AfterPosition(12), -1))
seqf.type = "test"
for codon_start in ["-1", "4", "NA"]:
seqf.qualifiers["codon_start"] = [codon_start]
with self.assertRaisesRegex(ValueError, "invalid codon_start"):
Feature.from_biopython(seqf)
def test_extends_past_after(self):
self.sub_locations[-1] = FeatureLocation(21,
AfterPosition(29),
strand=1)
self.cds.location = CompoundLocation(self.sub_locations)
new = self.cds.get_sub_location_from_protein_coordinates(0, 7)
assert new.end == 27
def test_after_position(self):
location = FeatureLocation(ExactPosition(1), AfterPosition(6), strand=1)
new_location = self.convert(location)
assert isinstance(new_location.start, ExactPosition)
assert new_location.start == 1
assert isinstance(new_location.end, AfterPosition)
assert new_location.end == 6
def test_simple(self):
location = FeatureLocation(0, AfterPosition(3), 1)
size = 9
assert not self.run(size, location, size - 3)
assert self.run(size, location, size - 2) # single ambiguous amino
assert self.run(size, location, size)
location = FeatureLocation(BeforePosition(3), 9, -1)
assert not self.run(size + 3, location, size)
assert self.run(size + 2, location, size) # single ambiguous amino
assert self.run(size, location, size)
def test_translation_outside_record(self):
rec = DummyRecord(seq="A" * 10)
for location in [
FeatureLocation(0, AfterPosition(6), strand=1),
FeatureLocation(BeforePosition(4), 10, strand=-1)
]:
bio = SeqFeature(location, type="CDS")
bio.qualifiers["translation"] = ["M" * 5]
with self.assertRaisesRegex(SecmetInvalidInputError,
"translation extends out of record"):
CDSFeature.from_biopython(bio, record=rec)
def test_compound(self):
location = CompoundLocation(
[FeatureLocation(0, 3),
FeatureLocation(6, 9)])
for good in ["A", "AA"]:
assert _is_valid_translation_length(good, location)
assert not _is_valid_translation_length("AAA", location)
# and with an ambiguous end, that becomes ok
location = CompoundLocation(
[FeatureLocation(0, 3),
FeatureLocation(6, AfterPosition(11))])
assert _is_valid_translation_length("AAA", location)
# and reversed ambiguous end
location = CompoundLocation([
FeatureLocation(BeforePosition(0), 3, -1),
FeatureLocation(6, 9, -1)
])
for good in ["A", "AA", "AAA"]:
assert _is_valid_translation_length(good, location)