def test_noncoding(self):
transcript = Transcript()
transcript.chrom = "Chr1"
transcript.source = "test"
transcript.start = 10000
transcript.end = 20000
exons = [(10000, 11500), (12000, 13000), (15000, 18000),
(19000, 20000)]
transcript.add_exons(exons)
transcript.strand = "+"
transcript.finalize()
logger = Mikado.utilities.log_utils.create_null_logger("correct_cds2")
copied = transcript.deepcopy()
trimmed = trim_noncoding(copied, max_length=50)
self.assertEqual(trimmed.start, 11450)
self.assertEqual(trimmed.end, 19050)
copied = transcript.deepcopy()
trimmed = trim_noncoding(copied, max_length=200)
self.assertEqual(trimmed.start, 11300)
self.assertEqual(trimmed.end, 19200)
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_correct_cds(self):
transcript = Transcript()
transcript.chrom = "Chr1"
transcript.source = "test"
transcript.start = 10000
transcript.end = 20000
exons = [(10000, 11500), (12000, 13000), (15000, 18000),
(19000, 20000)]
cds = [
(11400, 11500), # 101
(12000, 13000), # 1001 ==> 1102
(15000, 17998)
] # 2998 == > 3090 (y)
transcript.add_exons(exons)
transcript.add_exons(cds, features="CDS")
transcript.strand = "+"
transcript.finalize()
logger = Mikado.utilities.log_utils.create_null_logger("correct_cds")
copied = transcript.deepcopy()
trimmed = trim_coding(copied, logger, max_length=50)
self.assertEqual(trimmed.start, 11400)
self.assertEqual(trimmed.end, 19050)
copied = transcript.deepcopy()
self.assertEqual(copied.start, 10000)
trimmed = trim_coding(copied, logger, max_length=200)
self.assertEqual(trimmed.start, 11300)
self.assertEqual(trimmed.end, 19200)