def test_intronMatch(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 101
t2.end = 1600
t2.add_exons([(101, 500), (601, 700), (1001, 1320), (1451, 1460),
(1501, 1600)], "exon")
t2.add_exons([(401, 500), (601, 700), (1001, 1320), (1451, 1460),
(1501, 1510)], "CDS")
t2.finalize()
self.assertTrue(self.t1.is_coding)
self.assertTrue(t2.is_coding)
self.assertTrue(
MonosublocusHolder.is_intersecting(self.t1, t2,
logger=self.logger))
self.assertTrue(
MonosublocusHolder.is_intersecting(self.t1,
t2,
cds_only=True,
logger=self.logger))
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_no_overlap(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 1600
t2.end = 2000
t2.add_exons([(1600, 1700), (1801, 2000)])
t2.add_exons([(1661, 1700), (1801, 1850)], "CDS")
t2.finalize()
self.assertFalse(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_noIntronOverlap(self):
self.t1.strip_cds()
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 1250
t2.end = 2000
t2.add_exons([(1250, 1560), (1800, 2000)])
t2.finalize()
self.assertFalse(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_same_id(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G1.1"
t2.parent = "G1"
t2.start = 1250
t2.end = 2000
t2.add_exons([(1250, 1560), (1801, 2000)])
t2.add_exons([(1401, 1560), (1801, 1850)], "CDS")
t2.finalize()
# This fails because they have the same ID
self.assertFalse(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_intronOverlap(self):
self.t1.strip_cds()
t2 = Transcript()
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), (1420, 1470)])
t2.finalize()
self.assertTrue(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_not_intersecting(self):
# This one is contained and should be rejected
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 20
t2.id = "G1.1"
t2.parent = "G1"
t2.start = 601
t2.end = 1420
t2.add_exons([(601, 700), (1001, 1300), (1401, 1420)], "exon")
t2.add_exons([(601, 700), (1001, 1300), (1401, 1420)], "CDS")
t2.finalize()
self.assertEqual(
self.locus.is_alternative_splicing(t2)[:2], (False, "c"))
def testCdsOverlap(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
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.assertTrue(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_only_CDS_overlap(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
t2.id = "G2.1"
t2.parent = "G2"
t2.start = 1250
t2.end = 2000
t2.add_exons([(1250, 1560), (1801, 2000)])
t2.add_exons([(1401, 1560), (1801, 1850)], "CDS")
t2.finalize()
self.assertFalse(MonosublocusHolder.is_intersecting(self.t1, t2))
t2.strip_cds()
t2.finalized = False
t2.add_exons([(1461, 1560), (1801, 1850)], "CDS")
# No CDS overlap this time
self.assertFalse(MonosublocusHolder.is_intersecting(self.t1, t2))
def test_lowscore(self):
t2 = Transcript()
t2.chrom = "Chr1"
t2.strand = "+"
t2.score = 1
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)
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))
def test_valid_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.assertEqual(
self.locus.is_alternative_splicing(t2)[:2], (True, "J"))
self.locus.add_transcript_to_locus(t2)
self.assertEqual(len(self.locus.transcripts), 2,
self.locus.transcripts)