Python check_split_by_blast Examples

Example #1

    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)))

Example #2

File: test_splitting.py Project: wook2014/mikado

    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)