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_biopython_conversion(self):
bio = SeqFeature(FeatureLocation(1, 5))
bio.qualifiers["foo"] = ["bar"]
bio.qualifiers["key_only"] = None
# check that features without types are caught
with self.assertRaisesRegex(ValueError, "invalid length"):
sec = Feature.from_biopython(bio)
bio.type = "test"
sec = Feature.from_biopython(bio)
assert sec.get_qualifier("foo") == tuple(["bar"])
assert sec.get_qualifier("bar") is None
assert sec.get_qualifier("key_only") is True
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