def test_wrong_cds(self):
transcript = Transcript()
transcript.chrom = "15"
transcript.source = "protein_coding"
transcript.start = 47631264
transcript.end = 48051999
exons = [(47631264, 47631416), (47704590, 47704669),
(47762671, 47762742), (47893062, 47893093),
(47895572, 47895655), (48051942, 48051999)]
transcript.strand = "+"
transcript.add_exons(exons)
transcript.id = "ENST00000560636"
transcript.parent = "ENSG00000137872"
cds_line = "\t".join([
"15", "protein_coding", "CDS", "48051996", "48051996", ".", "+",
"0", "ID=ENST00000560636.cds1;Parent=ENST00000560636"
])
cds_line = GffLine(cds_line)
transcript.add_exon(cds_line)
logger = Mikado.utilities.log_utils.create_null_logger()
transcript.logger = logger
with self.assertLogs("null", level="WARNING"):
transcript.finalize()
trimmed = trim_coding(transcript, logger, max_length=50)
self.assertEqual(trimmed.start, 47631366)
self.assertEqual(trimmed.end, 48051992)
def test_non_redundant_as(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 20
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 101
t2.end = 1600
t2.add_exons([(101, 500), (601, 700), (1001, 1300), (1401, 1460),
(1501, 1600)], "exon")
t2.add_exons([(401, 500), (601, 700), (1001, 1300), (1401, 1440)],
"CDS")
t2.finalize()
self.locus.add_transcript_to_locus(t2)
self.assertEqual(len(self.locus.transcripts), 2,
self.locus.transcripts)
t3 = Transcript()
t3.chrom = "Chr1"
t3.strand = "+"
t3.score = 20
t3.id = "G3.1"
t3.parent = "G3"
t3.start = 201
t3.end = 1630
t3.add_exons([(201, 500), (601, 670), (1031, 1300), (1401, 1460),
(1501, 1630)], "exon")
t3.add_exons([(401, 500), (601, 670), (1031, 1300), (1401, 1440)],
"CDS")
t3.logger = self.logger
t3.finalize()
self.assertEqual(
self.locus.is_alternative_splicing(t3)[:2], (True, "j"))
self.locus.add_transcript_to_locus(t3)
self.assertEqual(len(self.locus.transcripts), 3,
self.locus.transcripts)
def test_noCDSOverlap(self):
self.t1.strip_cds()
self.assertEqual(self.t1.combined_cds_introns, set())
self.t1.finalized = False
self.t1.add_exons([(401, 500), (601, 700), (1001, 1100)], "CDS")
self.t1.finalize()
t2 = Transcript()
t2.logger = self.logger
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 101
t2.end = 1470
t2.add_exons([(101, 510), (601, 700), (960, 1350), (1421, 1470)])
t2.add_exons([(1201, 1350), (1421, 1450)], "CDS")
t2.finalize()
self.assertTrue(self.t1.is_coding)
self.assertTrue(t2.is_coding)
self.assertGreaterEqual(
0,
overlap((self.t1.combined_cds_start, self.t1.combined_cds_end),
(t2.combined_cds_start, t2.combined_cds_end)),
[(self.t1.combined_cds_start, self.t1.combined_cds_end),
(t2.combined_cds_start, t2.combined_cds_end)])
self.assertTrue(
MonosublocusHolder.is_intersecting(self.t1, t2,
logger=self.logger))
self.assertFalse(
MonosublocusHolder.is_intersecting(self.t1,
t2,
cds_only=True,
logger=self.logger))