def test_codon_finder_negative_3(self):
gtf_lines = """Chr5 TAIR10 mRNA 5335 5769 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 CDS 5697 5769 . - 0 transcript_id "AT5G01015.1"; gene_id "AT5G01015";;
Chr5 TAIR10 exon 5697 5769 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 CDS 5335 5576 . - 1 transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 exon 5335 5576 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";"""
gtf_lines = [GtfLine(_) for _ in gtf_lines.split("\n")]
t = Transcript(gtf_lines[0])
t.add_exons(gtf_lines[1:])
t.finalize()
seq = self.genome[t.chrom][t.start - 1:t.end]
correct_seq = "".join(
"""ATGGAGTCTAGCTTGCATAGTGTGATTTTCTTAGGTTTGCTTGCGACGATTCTGGTTACG
ACCAATGGCCAAGGAGACGGGACGGGGCTAAATGCAGAAGAAATGTGGCCAGTGGAGGTG
GGGATGGAGTATAGAGTATGGAGGAGAAAGCTGATGACGCCATTGGAGCTGTGCTTGGAG
TGCAAATGCTGCTCCTCCACCACTTGTGCCACCATGCCTTGCTGTTTCGGCATCAATTGC
CAGCTTCCCAACAAGCCATTTGGCGTTTGTGCCTTTGTTCCCAAGTCATGCCATTGTAAT
TCTTGCTCCATTTGA""".split("\n"))
logger = create_default_logger("test_codon_finder_negative_3",
level="WARNING")
tc = TranscriptChecker(t, seq, logger=logger)
tc.finalize()
correct_length = (5576 - 5335 + 1) + (5769 - 5697 + 1)
self.assertEqual(correct_length, len(correct_seq),
(correct_length, len(correct_seq)))
self.assertEqual(tc.cdna_length, correct_length,
(correct_length, tc.cdna_length))
self.assertEqual(len(tc.cdna), tc.cdna_length)
self.assertEqual(correct_seq, tc.cdna)
tc.check_orf()
tc_orfs = tc.find_overlapping_cds(tc.get_internal_orf_beds())
self.assertEqual(1, len(tc_orfs))
self.assertTrue(tc_orfs[0].has_stop_codon,
(tc_orfs[0], tc_orfs[0].stop_codon))
self.assertTrue(tc_orfs[0].has_start_codon,
(tc_orfs[0], tc_orfs[0].start_codon))
self.assertTrue(tc.is_coding)
self.assertIn("has_stop_codon", tc.attributes)
self.assertIn("has_start_codon", tc.attributes)
self.assertTrue(tc.has_start_codon, tc.cdna)
self.assertTrue(tc.has_stop_codon, tc.cdna)
def test_codon_finder_negative_strip_cds(self):
gtf_lines = """Chr5 TAIR10 mRNA 5335 5769 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 CDS 5697 5769 . - 0 transcript_id "AT5G01015.1"; gene_id "AT5G01015";;
Chr5 TAIR10 exon 5697 5769 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 CDS 5335 5576 . - 1 transcript_id "AT5G01015.1"; gene_id "AT5G01015";
Chr5 TAIR10 exon 5335 5576 . - . transcript_id "AT5G01015.1"; gene_id "AT5G01015";"""
gtf_lines = [GtfLine(_) for _ in gtf_lines.split("\n")]
t = Transcript(gtf_lines[0])
t.add_exons(gtf_lines[1:])
t.finalize()
seq = str(self.genome[t.chrom][t.start - 1:t.end])
# Basically insert an internal stop codon. This will make the ORF tests fail, leading to the ORF being stripped
seq = seq[:72] + Bio.Seq.reverse_complement("TAG") + seq[75:]
correct_seq = "".join(
"""ATGGAGTCTAGCTTGCATAGTGTGATTTTCTTAGGTTTGCTTGCGACGATTCTGGTTACG
ACCAATGGCCAAGGAGACGGGACGGGGCTAAATGCAGAAGAAATGTGGCCAGTGGAGGTG
GGGATGGAGTATAGAGTATGGAGGAGAAAGCTGATGACGCCATTGGAGCTGTGCTTGGAG
TGCAAATGCTGCTCCTCCACCACTTGTGCCACCATGCCTTGCTGTTTCGGCATCAATTGC
TAGCTTCCCAACAAGCCATTTGGCGTTTGTGCCTTTGTTCCCAAGTCATGCCATTGTAAT
TCTTGCTCCATTTGA""".split("\n"))
logger = create_default_logger("test_codon_finder_negative_3",
level="WARNING")
with self.assertRaises(InvalidTranscript):
for lenient in (False, True):
tc = TranscriptChecker(t,
seq,
logger=logger,
lenient=lenient,
strip_faulty_cds=False)
tc.finalize()
tc.check_orf()
for lenient in (False, True):
tc = TranscriptChecker(t,
seq,
logger=logger,
lenient=lenient,
strip_faulty_cds=True)
tc.finalize()
correct_length = (5576 - 5335 + 1) + (5769 - 5697 + 1)
self.assertEqual(correct_length, len(correct_seq),
(correct_length, len(correct_seq)))
self.assertEqual(tc.cdna_length, correct_length,
(correct_length, tc.cdna_length))
self.assertEqual(len(tc.cdna), tc.cdna_length)
self.assertEqual(correct_seq, tc.cdna)
tc.check_orf()
self.assertFalse(tc.is_coding)
tc_orfs = tc.find_overlapping_cds(tc.get_internal_orf_beds())
self.assertEqual(1, len(tc_orfs))
self.assertFalse(tc_orfs[0].has_stop_codon,
(tc_orfs[0], tc_orfs[0].stop_codon))
self.assertFalse(tc_orfs[0].has_start_codon,
(tc_orfs[0], tc_orfs[0].start_codon))
self.assertFalse(tc.is_coding)
self.assertNotIn("has_stop_codon", tc.attributes)
self.assertNotIn("has_start_codon", tc.attributes)
self.assertFalse(tc.has_start_codon, tc.cdna)
self.assertFalse(tc.has_stop_codon, tc.cdna)