def test_stringent_split(self): self.transcript.json_conf["pick"]["chimera_split"]["blast_check"] = True self.transcript.json_conf["pick"][ "chimera_split"]["blast_params"]["leniency"] = "STRINGENT" cds_boundaries = SortedDict() for orf in sorted(self.transcript.loaded_bed12, key=operator.attrgetter("thick_start", "thick_end")): cds_boundaries[(orf.thick_start, orf.thick_end)] = [orf] self.assertEqual(1, len(splitting.check_split_by_blast(self.transcript, cds_boundaries)))
def test_stringent_split(self): self.transcript.configuration.pick.chimera_split.blast_check = True self.transcript.configuration.pick.chimera_split.blast_params.leniency = "STRINGENT" cds_boundaries = SortedDict() for orf in sorted(self.transcript.loaded_bed12, key=operator.attrgetter("thick_start", "thick_end")): cds_boundaries[(orf.thick_start, orf.thick_end)] = [orf] self.assertEqual( 1, len(splitting.check_split_by_blast(self.transcript, cds_boundaries))) sl = loci.Superlocus(self.transcript, configuration=self.transcript.configuration) self.assertEqual(len(sl.transcripts), 1) sl.load_all_transcript_data() self.assertEqual(len(sl.transcripts), 1)