def test_subtype_recognition(self):
assert self.domain.domain_id
bio = self.domain.to_biopython()[0]
assert bio.qualifiers["aSTool"] == [TOOL]
assert bio.qualifiers["domain_id"]
new = AntismashDomain.from_biopython(bio)
assert isinstance(new, ModularDomain)
def test_conversion(self):
protein_location = FeatureLocation(0, 1)
domain = AntismashDomain(FeatureLocation(1, 3, 1), locus_tag="locus",
tool="test", protein_location=protein_location)
domain.domain_subtype = "subtest"
domain.specificity = ["a", "c", "f"]
domain.asf.add("first")
domain.asf.add("second")
assert domain.tool == "test"
assert domain.created_by_antismash
assert domain.locus_tag == "locus"
bio = domain.to_biopython()
assert len(bio) == 1
assert bio[0].qualifiers["aSTool"] == ["test"]
assert bio[0].qualifiers["tool"] == ["antismash"]
new_domain = AntismashDomain.from_biopython(bio[0])
assert new_domain.domain_subtype == domain.domain_subtype == "subtest"
assert new_domain.specificity == domain.specificity == ["a", "c", "f"]
assert new_domain.asf.hits == domain.asf.hits
assert new_domain.asf.hits == ["first", "second"]
assert new_domain.tool == domain.tool == "test"
assert new_domain.created_by_antismash
assert new_domain.locus_tag == "locus"
assert new_domain.protein_location == protein_location
def test_linebreaks(self):
self.domain.domain_id = "some-long-name.Condensation.1"
bio = self.domain.to_biopython()
# pretend a genbank was written and is being read back in
# but the line was long enough to cause a line break
bio[0].qualifiers["domain_id"][0] = self.domain.domain_id.replace(".", ". ")
new = AntismashDomain.from_biopython(bio[0])
assert new.domain_id == self.domain.domain_id
def test_conversion(self):
domain = self.domain
domain.asf.add("first")
domain.asf.add("second")
assert domain.tool == "test"
assert domain.created_by_antismash
assert domain.locus_tag == "locus"
bio = domain.to_biopython()
assert len(bio) == 1
assert bio[0].qualifiers["aSTool"] == ["test"]
assert bio[0].qualifiers["tool"] == ["antismash"]
new_domain = AntismashDomain.from_biopython(bio[0])
assert new_domain.asf.hits == domain.asf.hits
assert new_domain.asf.hits == ["first", "second"]
assert new_domain.tool == domain.tool == "test"
assert new_domain.created_by_antismash
assert new_domain.locus_tag == "locus"
assert new_domain.protein_location == self.protein_location
def test_subvariant_detection(self):
bio = self.rre.to_biopython()[0]
new = AntismashDomain.from_biopython(bio)
assert isinstance(new, RREDomain)