def find_similar(self, gfe, features, imgtdb_version):
"""
creates GFE from HLA sequence and locus
:param locus: string containing HLA locus.
:param sequence: string containing sequence data.
:return: GFEobject.
"""
if is_classI(gfe):
gfe_dict = self.breakup_gfe(gfe)
[locus, feature_accessions] = gfe.split("w")
if self.gfe2hla:
exon23 = "-".join([gfe_dict["EXON-2"], gfe_dict["EXON-3"]])
df = self.gfe2hla[locus][(self.gfe2hla[locus]['EXON23'] == exon23) & (self.gfe2hla[locus]['DB'] == imgtdb_version)][['GFE', 'HLA']]\
.reset_index()
return self.create_typing(df, gfe, features)
else:
cypher = similar_gfe_classI(gfe, gfe_dict["EXON-2"],
gfe_dict["EXON-3"],
imgtdb_version)
similar_data = self.graph.run(cypher).to_data_frame()
return self.create_typing(similar_data, gfe, features)
elif is_classII(gfe):
gfe_dict = self.breakup_gfe(gfe)
[locus, feature_accessions] = gfe.split("w")
if self.gfe2hla:
exon2 = gfe_dict["EXON-2"]
df = self.gfe2hla[locus][(self.gfe2hla[locus]['EXON2'] == exon2) & (self.gfe2hla[locus]['DB'] == imgtdb_version)][['GFE', 'HLA']]\
.reset_index()
return self.create_typing(df, gfe, features)
else:
cypher = similar_gfe_classII(gfe, gfe_dict["EXON-2"],
imgtdb_version)
similar_data = self.graph.run(cypher).to_data_frame()
return self.create_typing(similar_data, gfe, features)
elif is_kir(gfe):
return self.find_gfe_kir(gfe, features)
else:
return
def test_002_iskir(self):
self.assertTrue(is_kir('KIR*3DL1'))
self.assertFalse(is_kir('exon-3'))
pass