def test_sequence_conversion(self): pseq = PX.Sequence( type="protein", # id_ref=None, # id_source=None, symbol="ADHX", accession=PX.Accession("P81431", source="UniProtKB"), name="Alcohol dehydrogenase class-3", # location=None, mol_seq=PX.MolSeq( "TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD"), uri=None, annotations=[ PX.Annotation(ref="EC:1.1.1.1"), PX.Annotation(ref="GO:0004022") ], domain_architecture=PX.DomainArchitecture( length=50, domains=[ PX.ProteinDomain(*args) for args in ( # value, start, end, confidence ("FOO", 0, 5, 7.0e-26), ("BAR", 8, 13, 7.2e-117), ("A-OK", 21, 34, 2.4e-06), ("WD40", 40, 50, 0.3)) ], )) srec = pseq.to_seqrecord() # TODO: check seqrec-specific traits (see args) # Seq(letters, alphabet), id, name, description, features pseq2 = PX.Sequence.from_seqrecord(srec)
def domain(self, elem): """Create protein domain object.""" return PX.ProteinDomain(elem.text.strip(), int(elem.get('from')) - 1, int(elem.get('to')), confidence=_float(elem.get('confidence')), id=elem.get('id'))
def test_sequence_conversion(self): pseq = PX.Sequence( type='protein', # id_ref=None, # id_source=None, symbol='ADHX', accession=PX.Accession('P81431', source='UniProtKB'), name='Alcohol dehydrogenase class-3', # location=None, mol_seq=PX.MolSeq( 'TDATGKPIKCMAAIAWEAKKPLSIEEVEVAPPKSGEVRIKILHSGVCHTD'), uri=None, annotations=[ PX.Annotation(ref='EC:1.1.1.1'), PX.Annotation(ref='GO:0004022') ], domain_architecture=PX.DomainArchitecture( length=50, domains=[ PX.ProteinDomain(*args) for args in ( # value, start, end, confidence ('FOO', 0, 5, 7.0e-26), ('BAR', 8, 13, 7.2e-117), ('A-OK', 21, 34, 2.4e-06), ('WD40', 40, 50, 0.3)) ], )) srec = pseq.to_seqrecord() # TODO: check seqrec-specific traits (see args) # Seq(letters, alphabet), id, name, description, features pseq2 = PX.Sequence.from_seqrecord(srec)
def domain(self, elem): """Create protein domain object.""" return PX.ProteinDomain(elem.text.strip(), int(elem.get("from")) - 1, int(elem.get("to")), confidence=_float(elem.get("confidence")), id=elem.get("id"))