class TestCDSBiopythonConversion(unittest.TestCase):
def setUp(self):
self.cds = CDSFeature(FeatureLocation(0, 12, 1),
translation="A" * 4,
locus_tag="loctag",
gene="gene",
protein_id="prot_id")
def convert(self):
bio_features = self.cds.to_biopython()
assert isinstance(bio_features, list)
assert len(bio_features) == 1
return bio_features[0]
def test_basics(self):
bio = self.convert()
assert bio.location == self.cds.location
assert bio.qualifiers["locus_tag"] == ["loctag"]
assert bio.qualifiers["gene"] == ["gene"]
assert bio.qualifiers["protein_id"] == ["prot_id"]
assert bio.qualifiers["translation"] == ["A" * 4]
regen = CDSFeature.from_biopython(bio)
assert regen.location == self.cds.location
assert regen.locus_tag == self.cds.locus_tag
assert regen.gene == self.cds.gene
assert regen.protein_id == self.cds.protein_id
def test_without_genefunctions(self):
bio = self.convert()
assert "gene_functions" not in bio.qualifiers
assert "gene_kind" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.gene_functions
def test_with_genefunctions(self):
self.cds.gene_functions.add(GeneFunction.ADDITIONAL, "testtool",
"dummy")
bio = self.convert()
assert "gene_functions" in bio.qualifiers
assert bio.qualifiers["gene_kind"] == [str(
self.cds.gene_function)] == ["biosynthetic-additional"]
regen = CDSFeature.from_biopython(bio)
assert regen.gene_function == self.cds.gene_function
assert regen.gene_functions.get_by_tool(
"testtool") == self.cds.gene_functions.get_by_tool("testtool")
def test_without_secmet(self):
assert not self.cds.sec_met
bio = self.convert()
assert "sec_met" not in bio.qualifiers # for detecting legacy versions
assert "sec_met_domain" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.sec_met
def test_with_secmet(self):
domains = [
SecMetQualifier.Domain("testA", 0.1, 1.1, 3, "test"),
SecMetQualifier.Domain("testB", 5.1, 3.9, 5, "dummy")
]
self.cds.sec_met = SecMetQualifier(domains)
bio = self.convert()
assert "sec_met" not in bio.qualifiers # again, detecting leftover legacy versions
assert len(bio.qualifiers["sec_met_domain"]) == 2
assert bio.qualifiers["sec_met_domain"] == list(map(str, domains))
regen = CDSFeature.from_biopython(bio)
assert regen.sec_met
assert len(regen.sec_met.domains) == len(domains)
assert regen.sec_met.domains == domains
def test_mixed_strand(self):
bio = self.cds.to_biopython()[0]
for location in [
CompoundLocation([
FeatureLocation(1, 5, strand=-1),
FeatureLocation(8, 10, strand=1)
]),
CompoundLocation([
FeatureLocation(1, 5, strand=1),
FeatureLocation(8, 10, strand=None)
])
]:
bio.location = location
with self.assertRaisesRegex(
ValueError, "compound locations with mixed strands"):
CDSFeature.from_biopython(bio)
class TestCDSBiopythonConversion(unittest.TestCase):
def setUp(self):
self.cds = CDSFeature(FeatureLocation(0, 12, 1),
translation="A" * 4,
locus_tag="loctag",
gene="gene",
protein_id="prot_id")
def convert(self):
bio_features = self.cds.to_biopython()
assert isinstance(bio_features, list)
assert len(bio_features) == 1
return bio_features[0]
def test_basics(self):
bio = self.convert()
assert bio.location == self.cds.location
assert bio.qualifiers["locus_tag"] == ["loctag"]
assert bio.qualifiers["gene"] == ["gene"]
assert bio.qualifiers["protein_id"] == ["prot_id"]
assert bio.qualifiers["translation"] == ["A" * 4]
regen = CDSFeature.from_biopython(bio)
assert regen.location == self.cds.location
assert regen.locus_tag == self.cds.locus_tag
assert regen.gene == self.cds.gene
assert regen.protein_id == self.cds.protein_id
def test_without_genefunctions(self):
bio = self.convert()
assert "gene_functions" not in bio.qualifiers
assert "gene_kind" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.gene_functions
def test_with_genefunctions(self):
self.cds.gene_functions.add(GeneFunction.ADDITIONAL, "testtool",
"dummy")
bio = self.convert()
assert "gene_functions" in bio.qualifiers
assert bio.qualifiers["gene_kind"] == [str(
self.cds.gene_function)] == ["biosynthetic-additional"]
regen = CDSFeature.from_biopython(bio)
assert regen.gene_function == self.cds.gene_function
assert regen.gene_functions.get_by_tool(
"testtool") == self.cds.gene_functions.get_by_tool("testtool")
def test_without_secmet(self):
assert not self.cds.sec_met
bio = self.convert()
assert "sec_met" not in bio.qualifiers # for detecting legacy versions
assert "sec_met_domain" not in bio.qualifiers
regen = CDSFeature.from_biopython(bio)
assert not regen.sec_met
def test_with_secmet(self):
domains = [
SecMetQualifier.Domain("testA", 0.1, 1.1, 3, "test"),
SecMetQualifier.Domain("testB", 5.1, 3.9, 5, "dummy")
]
self.cds.sec_met = SecMetQualifier(domains)
bio = self.convert()
assert "sec_met" not in bio.qualifiers # again, detecting leftover legacy versions
assert len(bio.qualifiers["sec_met_domain"]) == 2
assert bio.qualifiers["sec_met_domain"] == list(map(str, domains))
regen = CDSFeature.from_biopython(bio)
assert regen.sec_met
assert len(regen.sec_met.domains) == len(domains)
assert regen.sec_met.domains == domains
def test_mixed_strand(self):
bio = self.cds.to_biopython()[0]
for location in [
CompoundLocation([
FeatureLocation(1, 5, strand=-1),
FeatureLocation(8, 10, strand=1)
]),
CompoundLocation([
FeatureLocation(1, 5, strand=1),
FeatureLocation(8, 10, strand=None)
])
]:
bio.location = location
with self.assertRaisesRegex(
ValueError, "compound locations with mixed strands"):
CDSFeature.from_biopython(bio)
# compound locations starting with an invalid strand will be treated as per a non-compound wtih a bad strand
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_invalid_translation_table(self):
bio = self.cds.to_biopython()[0]
bio.qualifiers["transl_table"] = ["11a"]
with self.assertRaisesRegex(SecmetInvalidInputError,
"invalid translation table"):
CDSFeature.from_biopython(bio)
