def test_spanning_hit_lenient(self):
self.transcript.blast_hits = [self.get_spanning_hit()]
self.transcript.json_conf["pick"]["chimera_split"][
"blast_check"] = True
self.transcript.json_conf["pick"]["chimera_split"]["blast_params"][
"leniency"] = "LENIENT"
self.assertEqual(1, len(list(splitting.split_by_cds(self.transcript))))
def test_lenient_split_twohits(self):
hit2 = self.get_second_hit()
self.transcript.blast_hits.append(hit2)
self.transcript.json_conf["pick"]["chimera_split"][
"blast_check"] = True
self.transcript.json_conf["pick"]["chimera_split"]["blast_params"][
"leniency"] = "LENIENT"
self.assertEqual(2, len(list(splitting.split_by_cds(self.transcript))))
def test_spanning_hit_nocheck(self):
self.transcript.blast_hits = [self.get_spanning_hit()]
self.transcript.json_conf["pick"]["chimera_split"][
"blast_check"] = False
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(len(cds_boundaries), 2)
self.assertEqual(self.transcript.number_internal_orfs, 2)
self.assertEqual(2, len(list(splitting.split_by_cds(self.transcript))))
def test_deleted_hits(self):
delattr(self.transcript, "blast_hits")
self.transcript.json_conf["pick"]["chimera_split"][
"blast_check"] = True
self.transcript.json_conf["pick"]["chimera_split"]["blast_params"][
"leniency"] = "LENIENT"
self.transcript.logger = self.logger
with self.assertLogs("null", level="WARNING") as log_split:
self.assertEqual(
2, len(list(splitting.split_by_cds(self.transcript))))
self.assertIn(
"WARNING:null:BLAST hits store lost for transcript1! Creating a mock one to avoid a crash",
log_split.output)
def test_simple_split(self):
"""
Check that the original transcript can be split in two
:return:
"""
self.assertIsNotNone(self.transcript.json_conf)
self.assertIn("pick", self.transcript.json_conf)
self.transcript.json_conf["pick"]["chimera_split"][
"blast_check"] = False
# with self.assertLogs("test_mono", level="DEBUG") as log_split:
new_transcripts = list(splitting.split_by_cds(self.transcript))
# print(log_split.output)
# self.assertIn("DEBUG:test_mono:",
# log_split.output)
self.assertEqual(len(new_transcripts), 2,
"\n".join(str(_) for _ in new_transcripts))
self.assertEqual(new_transcripts[0].start, self.transcript.start)
self.assertEqual(new_transcripts[1].end, self.transcript.end)