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)