def test_b3_seq(self):
b3 = bed12.BED12(self.bed3,
transcriptomic=True,
fasta_index=self.index)
self.assertFalse(b3.invalid,
(len(b3), len(self.index[b3.id]), b3.invalid_reason,
(b3.thick_end, b3.thick_start),
(b3.thick_end - b3.thick_start + 1) % 3))
def test_3_partial(self):
line = "\t".join([
'class_Chr1.1004.0', '0', '1060',
'ID=class_Chr1.1004.0|m.22214;class_Chr1.1004.0|g.22214;ORF_class_Chr1.1004.0|g.22214_class_Chr1.1004.0|m.22214_type:3prime_partial_len:300_(+)',
'0', '+', '162', '1060', '0', '1', '1060', '0'
])
bed_line = bed12.BED12(line, transcriptomic=True)
self.assertFalse(bed_line.invalid, bed_line.invalid_reason)
def test_regression(self):
sequence = """TC
CTCACAGTTACTATAAGCTCGTCT
ATGGCCAGAGACGGTGGTGTTTCTTGTTTACGAA
GGTCGGAGATGATGAGCGTCGGTGGTATCGGAGGAATTGAATCTGCGCCGTTGGATTTAG
ATGAAGTTCATGTCTTAGCCGTTGATGACAGTCTCGTTGATCGTATTGTCATCGAGAGAT
TGCTTCGTATTACTTCCTGCAAAGTTACGGCGGTAGATAGTGGATGGCGTGCTCTGGAAT
TTCTAGGGTTAGATAATGAGAAAGCTTCTGCTGAATTCGATAGATTGAAAGTTGATTTGA
TCATCACTGATTACTGTATGCCTGGAATGACTGGTTATGAGCTTCTCAAGAAGATTAAGG
AATCGTCCAATTTCAGAGAAGTTCCGGTTGTAATCATGTCGTCGGAGAATGTATTGACCA
GAATCGACAGATGCCTTGAGGAAGGTGCTCAAGATTTCTTATTGAAACCGGTGAAACTCG
CCGACGTGAAACGTCTGAGAAGTCATTTAACTAAAGACGTTAAACTTTCCAACGGAAACA
AACGGAAGCTTCCGGAAGATTCTAGTTCCGTTAACTCTTCGCTTCCTCCACCGTCACCTC
CGTTGACTATCTCGCCTGA"""
record = SeqRecord.SeqRecord(Seq.Seq(sub("\n", "", sequence)),
id="class_Chr1.1006.0")
index = {record.id: record}
line = "\t".join([
'class_Chr1.1006.0', '0', '619',
'ID=class_Chr1.1006.0|m.22308;class_Chr1.1006.0|g.22308;ORF_class_Chr1.1006.0|g.22308_class_Chr1.1006.0|m.22308_type:internal_len:206_(+)',
'0', '+', '2', '617', '0', '1', '619', '0'
])
# Now we are going back to find the start codon
bed_line = bed12.BED12(line,
transcriptomic=True,
fasta_index=index,
max_regression=0.2)
self.assertFalse(bed_line.invalid, bed_line.invalid_reason)
self.assertEqual(bed_line.phase, 0)
# Start codon in frame found at location 27
self.assertEqual(bed_line.thick_start, 27)
self.assertTrue(bed_line.has_start_codon)
self.assertFalse(bed_line.has_stop_codon)
lines = """Chr1 CLASS transcript 3442811 3443785 1000 - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0"; exon_number "1"; Abundance "22.601495"; canonical_proportion "1.0";
Chr1 CLASS exon 3442811 3442999 . - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0";
Chr1 CLASS exon 3443099 3443169 . - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0";
Chr1 CLASS exon 3443252 3443329 . - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0";
Chr1 CLASS exon 3443417 3443493 . - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0";
Chr1 CLASS exon 3443582 3443785 . - . gene_id "Chr1.1006.gene"; transcript_id "class_Chr1.1006.0";"""
lines = [GTF.GtfLine(_) for _ in lines.split("\n") if _]
transcript = Transcript(lines[0])
transcript.add_exons(lines[1:])
transcript.finalize()
transcript.load_orfs([bed_line])
self.assertTrue(transcript.is_coding)
self.assertTrue(transcript.has_start_codon)
self.assertFalse(transcript.has_stop_codon)
self.assertEqual(transcript.selected_cds_end, transcript.start)
self.assertEqual(transcript.selected_cds_start, transcript.end - 26)
def test_relocation(self):
bed = bed12.BED12(self.bed_row,
fasta_index=self.index,
transcriptomic=True,
max_regression=0.3)
# print(self.seq[bed.thick_start-1:bed.thick_end].seq.translate())
self.assertEqual(bed.thick_start, 195)
self.assertEqual(bed.phase, 0)
def test_b4_seq(self):
b4 = bed12.BED12(self.bed4,
transcriptomic=True,
fasta_index=self.index)
self.assertFalse(b4.invalid,
(len(b4), b4.invalid_reason, len(self.index[b4.id])))
self.assertTrue(b4.has_start_codon)
self.assertTrue(b4.has_stop_codon)
self.assertTrue(b4.thick_start, 641)
self.assertTrue(b4.thick_end, 1112)
self.assertTrue(b4.cds_len, 1112 - 641)
def test_b2_seq_no_start(self):
b2 = bed12.BED12(self.bed2,
transcriptomic=True,
fasta_index=self.index,
max_regression=0)
self.assertNotIn(str(self.index[b2.chrom][766 + 3:766 + 6].seq),
("TAG", "TGA", "TAA"))
self.assertEqual(b2.start, 1)
self.assertEqual(len(b2), 809)
self.assertFalse(
b2.has_start_codon,
(b2.thick_start, b2.thick_end, self.bed2.split("\t")[6:8],
self.index[b2.chrom][b2.thick_start + (3 - b2.phase - 1) % 3 -
1:b2.thick_end].seq.translate()))
def test_b1_seq(self):
b1 = bed12.BED12(self.bed1,
transcriptomic=True,
fasta_index=self.index)
self.assertIn(str(self.index[b1.chrom][386 + 3:386 + 6].seq),
("TAG", "TGA", "TAA"))
self.assertEqual(b1.start, 1)
self.assertEqual(len(b1), 784)
self.assertEqual(
"ATG",
str(self.index[b1.chrom][b1.thick_start - 1:b1.thick_start +
2].seq),
str(self.index[b1.chrom][b1.thick_start - 1:b1.thick_start +
2].seq))
self.assertEqual("ATG", b1.start_codon, b1.start_codon)
self.assertEqual(b1.thick_start, 30)
self.assertEqual(b1.thick_end, 386)
self.assertTrue(b1.has_stop_codon)
def test_b4(self):
b4 = bed12.BED12(self.bed4, transcriptomic=True)
self.assertFalse(b4.invalid)
self.assertEqual(b4.start, 1)
self.assertEqual(len(b4), 3604)
self.assertEqual(b4.cds_len, 1115 - 641, (b4.cds_len, 1115 - 641))
def test_b3(self):
b3 = bed12.BED12(self.bed3, transcriptomic=True)
self.assertFalse(b3.invalid)
self.assertEqual(b3.start, 1)
self.assertEqual(len(b3), 3683)
def test_b2(self):
b2 = bed12.BED12(self.bed2, transcriptomic=True)
self.assertEqual(b2.start, 1)
self.assertEqual(len(b2), 809)
self.assertEqual(b2.thick_start, 2)
self.assertEqual(b2.thick_end, 766)
def test_b1(self):
b1 = bed12.BED12(self.bed1, transcriptomic=True)
self.assertEqual(b1.start, 1)
self.assertEqual(len(b1), 784)
self.assertEqual(b1.thick_start, 30)
self.assertEqual(b1.thick_end, 386)