class TestRetrieval(unittest.TestCase):
def setUp(self):
self.tr = Transcript()
self.tr.chrom = "Chr1"
self.tr.start = 101
self.tr.end = 2000
self.tr.strand = None
self.tr.add_exons([(101, 2000)])
self.tr.id = "test1"
self.tr.parent = "gene1"
self.tr.finalize()
conf = to_json(os.path.join(
os.path.dirname(__file__),
"configuration.yaml"
))
self.assertTrue(conf["pick"]["chimera_split"]["blast_check"])
self.assertTrue(conf["pick"]["chimera_split"]["execute"])
self.assertEqual(conf["pick"]["chimera_split"]["blast_params"]["leniency"],
"LENIENT")
conf["pick"]["orf_loading"]["minimal_secondary_orf_length"] = 50
self.tr.json_conf = conf
def test_load_pos_and_neg(self):
b1 = BED12(transcriptomic=True)
b1.chrom = self.tr.id
b1.start = 0
b1.end = self.tr.cdna_length - 1
b1.strand = "+"
b1.name = "first"
b1.thick_start = 101
b1.thick_end = 190
self.assertFalse(b1.invalid)
b2 = b1.copy()
b2.strand = "-"
b2.thick_start = 1
b2.thick_end = 87
b2.name = "second"
self.assertFalse(b2.invalid)
with self.assertLogs("null", "DEBUG") as _:
after_overlap_check = retrieval.find_overlapping_cds(self.tr, [b1, b2])
# print(*_.output, sep="\n")
self.assertEqual(len(after_overlap_check), 2, self.tr.json_conf["pick"]["orf_loading"])
self.assertEqual(after_overlap_check,
[b1, b2],
[_.name for _ in after_overlap_check])
retrieval.load_orfs(self.tr, [b1, b2])
self.assertEqual(self.tr.number_internal_orfs, 1)
self.assertEqual(self.tr.combined_cds_start, 201, self.tr.combined_cds_start)
self.assertEqual(self.tr.combined_cds_length, 90)
def test_connect(self):
retrieval._connect_to_db(self.tr)
reflector = reflection.Inspector.from_engine(self.tr.engine)
def test_mixed_strands(self):
"""Verify that no retained intron is called if the strands are mixed."""
t1 = Transcript()
t1.chrom, t1.strand, t1.id = 1, "+", "t1"
t1.add_exons([(101, 500), (801, 1000), (1201, 1300), (1501, 1800)])
t1.add_exons(
[
(201, 500), # 300
(801, 1000), # 200
(1201, 1300), # 100
(1501, 1530) # 30
],
features="CDS")
t1.finalize()
t2 = Transcript()
t2.chrom, t2.strand, t2.id = 1, "-", "t2"
t2.add_exons([(601, 1000), (1201, 1300), (1501, 1800)])
t2.add_exons(
[
(1501, 1530), # 30
(1201, 1300), # 100
(771, 1000) # 230
],
features="CDS")
t2.finalize()
sup = Superlocus(t1, json_conf=self.my_json, stranded=False)
sup.add_transcript_to_locus(t2)
sup.find_retained_introns(t2)
self.assertEqual(sup.transcripts["t2"].retained_intron_num, 0)
def test_non_coding_negative(self):
tr = Transcript()
tr.chrom = "Chr1"
tr.start = 101
tr.end = 2000
tr.strand = "-"
tr.add_exons([(101, 300),
(1701, 2000)])
tr.id = "test1"
tr.parent = "gene1"
tr.finalize()
gff = tr.format("gff", with_introns=True)
self.maxDiff = None
res = """Chr1\tMikado\ttranscript\t101\t2000\t.\t-\t.\tID=test1;Parent=gene1
Chr1\tMikado\texon\t101\t300\t.\t-\t.\tID=test1.exon1;Parent=test1
Chr1\tMikado\tintron\t301\t1700\t.\t-\t.\tID=test1.intron1;Parent=test1
Chr1\tMikado\texon\t1701\t2000\t.\t-\t.\tID=test1.exon2;Parent=test1"""
self.assertEqual(gff,
res,
"++++\n\n"+"\n+++\n".join([gff, res]))
gtf = tr.format("gtf", with_introns=True)
res = """Chr1\tMikado\ttranscript\t101\t2000\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\texon\t101\t300\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\tintron\t301\t1700\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\texon\t1701\t2000\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";"""
self.assertEqual(gtf, res,
"++++\n\n" + "\n+++\n".join([gtf, res]))
class TestRetrieval(unittest.TestCase):
def setUp(self):
self.tr = Transcript()
self.tr.chrom = "Chr1"
self.tr.start = 101
self.tr.end = 2000
self.tr.strand = None
self.tr.add_exons([(101, 2000)])
self.tr.id = "test1"
self.tr.parent = "gene1"
self.tr.finalize()
conf = to_json(
os.path.join(os.path.dirname(__file__), "configuration.yaml"))
self.assertTrue(conf["pick"]["chimera_split"]["blast_check"])
self.assertTrue(conf["pick"]["chimera_split"]["execute"])
self.assertEqual(
conf["pick"]["chimera_split"]["blast_params"]["leniency"],
"LENIENT")
conf["pick"]["orf_loading"]["minimal_secondary_orf_length"] = 50
self.tr.json_conf = conf
def test_load_pos_and_neg(self):
b1 = BED12(transcriptomic=True)
b1.chrom = self.tr.id
b1.start = 0
b1.end = self.tr.cdna_length - 1
b1.strand = "+"
b1.name = "first"
b1.thick_start = 101
b1.thick_end = 190
self.assertFalse(b1.invalid)
b2 = b1.copy()
b2.strand = "-"
b2.thick_start = 1
b2.thick_end = 87
b2.name = "second"
self.assertFalse(b2.invalid)
with self.assertLogs("null", "DEBUG") as _:
after_overlap_check = retrieval.find_overlapping_cds(
self.tr, [b1, b2])
# print(*_.output, sep="\n")
self.assertEqual(len(after_overlap_check), 2,
self.tr.json_conf["pick"]["orf_loading"])
self.assertEqual(after_overlap_check, [b1, b2],
[_.name for _ in after_overlap_check])
retrieval.load_orfs(self.tr, [b1, b2])
self.assertEqual(self.tr.number_internal_orfs, 1)
self.assertEqual(self.tr.combined_cds_start, 201,
self.tr.combined_cds_start)
self.assertEqual(self.tr.combined_cds_length, 90)
def test_connect(self):
retrieval._connect_to_db(self.tr)
reflector = reflection.Inspector.from_engine(self.tr.engine)
def test_real_retained_pos_noCDS(self):
"""Here we verify that a real retained intron is called as such, even when the transcript lacks a CDS"""
t1 = Transcript()
t1.chrom, t1.strand, t1.id = 1, "+", "t1"
t1.add_exons([(101, 500), (801, 1000), (1201, 1300), (1501, 1800)])
t1.add_exons(
[
(201, 500), # 300
(801, 1000), # 200
(1201, 1300), # 100
(1501, 1530) # 30
],
features="CDS")
t1.finalize()
t2 = Transcript()
t2.chrom, t2.strand, t2.id = 1, "+", "t2"
t2.add_exons([(101, 500), (801, 1000), (1201, 1600)])
# t2.add_exons([(201, 500), # 300
# (801, 1000), # 200
# (1201, 1420), # 220
# ], features="CDS")
t2.finalize()
sup = Superlocus(t1, json_conf=self.my_json)
sup.add_transcript_to_locus(t2)
sup.find_retained_introns(t2)
self.assertEqual(sup.transcripts["t2"].retained_introns,
((1201, 1600), ))
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_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_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_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_non_coding_negative(self):
tr = Transcript()
tr.chrom = "Chr1"
tr.start = 101
tr.end = 2000
tr.strand = "-"
tr.add_exons([(101, 300), (1701, 2000)])
tr.id = "test1"
tr.parent = "gene1"
tr.finalize()
gff = tr.format("gff", with_introns=True)
self.maxDiff = None
res = """Chr1\tMikado\ttranscript\t101\t2000\t.\t-\t.\tID=test1;Parent=gene1
Chr1\tMikado\texon\t101\t300\t.\t-\t.\tID=test1.exon1;Parent=test1
Chr1\tMikado\tintron\t301\t1700\t.\t-\t.\tID=test1.intron1;Parent=test1
Chr1\tMikado\texon\t1701\t2000\t.\t-\t.\tID=test1.exon2;Parent=test1"""
self.assertEqual(gff, res, "++++\n\n" + "\n+++\n".join([gff, res]))
gtf = tr.format("gtf", with_introns=True)
res = """Chr1\tMikado\ttranscript\t101\t2000\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\texon\t101\t300\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\tintron\t301\t1700\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";
Chr1\tMikado\texon\t1701\t2000\t.\t-\t.\tgene_id "gene1"; transcript_id "test1";"""
self.assertEqual(gtf, res, "++++\n\n" + "\n+++\n".join([gtf, res]))
def test_exon_switching_pos_noCDS(self):
"""Checking that an exon switching is treated correctly as a NON-retained intron even when the CDS is absent.
Positive strand case"""
t1 = Transcript()
t1.chrom, t1.strand, t1.id = 1, "+", "t1"
t1.add_exons([(101, 500), (801, 1000), (1201, 1300), (2501, 2800)])
t1.add_exons(
[
(201, 500), # 300
(801, 1000), # 200
(1201, 1300), # 100
(2501, 2530) # 30
],
features="CDS")
t1.finalize()
t2 = Transcript()
t2.chrom, t2.strand, t2.id = 1, "+", "t2"
t2.add_exons([(101, 500), (801, 1000), (1201, 1300), (1501, 1800)])
# t2.add_exons([(201, 500), # 300
# (801, 1000), # 200
# (1201, 1300), # 100
# (1501, 1530) # 30
# ], features="CDS")
t2.finalize()
sup = Superlocus(t1, json_conf=self.my_json)
sup.add_transcript_to_locus(t2)
sup.find_retained_introns(t2)
self.assertEqual(sup.transcripts["t2"].retained_intron_num, 0,
sup.transcripts["t2"].retained_introns)
def test_not_retained_neg(self):
"""Here we verify that a false retained intron is not called as such"""
t1 = Transcript()
t1.chrom, t1.strand, t1.id = 1, "-", "t1"
t1.add_exons([(101, 500), (801, 1000), (1201, 1300), (1501, 1800)])
t1.add_exons(
[
(201, 500), # 300
(801, 1000), # 200
(1201, 1300), # 100
(1501, 1530) # 30
],
features="CDS")
t1.finalize()
t2 = Transcript()
t2.chrom, t2.strand, t2.id = 1, "-", "t2"
t2.add_exons([(301, 1000), (1201, 1300), (1501, 1800)])
t2.add_exons(
[
(1501, 1530), # 30
(1201, 1300), # 100
(471, 1000) # 230
],
features="CDS")
t2.finalize()
sup = Superlocus(t1, json_conf=self.my_json)
sup.add_transcript_to_locus(t2)
sup.find_retained_introns(t2)
self.assertEqual(sup.transcripts["t2"].retained_intron_num, 0)
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_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_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_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_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_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_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_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_locus(self):
"""Basic testing of the Locus functionality."""
logger = create_null_logger("null")
logger.setLevel("WARNING")
logger.info("Started")
slocus = Superlocus(self.transcript1,
json_conf=self.my_json,
logger=logger)
slocus.add_transcript_to_locus(self.transcript2)
self.assertEqual(slocus.strand, self.transcript1.strand)
self.assertEqual(slocus.start,
min(self.transcript1.start, self.transcript2.start))
self.assertEqual(slocus.end,
max(self.transcript1.end, self.transcript2.end))
logger.info(slocus.transcripts)
slocus.define_subloci()
logger.info(slocus.subloci)
logger.info(slocus.transcripts)
self.assertEqual(len(slocus.transcripts), 2)
self.assertEqual(len(slocus.subloci), 2)
slocus.define_monosubloci()
self.assertEqual(len(slocus.monosubloci), 2)
slocus.define_loci()
self.assertEqual(len(slocus.loci), 1)
self.assertEqual(
list(slocus.loci[list(
slocus.loci.keys())[0]].transcripts.keys())[0], "t0")
gff_transcript3 = """Chr1\tfoo\ttranscript\t101\t200\t.\t-\t.\tID=tminus0
Chr1\tfoo\texon\t101\t200\t.\t-\t.\tID=tminus0:exon1;Parent=tminus0""".split(
"\n")
gff_transcript3 = [GFF.GffLine(x) for x in gff_transcript3]
transcript3 = Transcript(gff_transcript3[0])
for exon in gff_transcript3[1:]:
transcript3.add_exon(exon)
transcript3.finalize()
minusuperlocus = Superlocus(transcript3, json_conf=self.my_json)
minusuperlocus.define_loci()
self.assertEqual(len(minusuperlocus.loci), 1)
self.assertTrue(transcript3.strand != self.transcript1.strand)
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_caseNegative(self):
tr = Transcript()
tr.chrom, tr.start, tr.end, tr.strand = "Chr1", 101, 3000, "-"
tr.id = "test1"
tr.add_exons([(101, 300),
(401, 600),
(801, 1200),
(2501, 3000)
])
tr.add_exons([(421, 600), # 180
(801, 1200), # 400
(2501, 2700) # 200 = 780 % 3 == 0
], features="CDS")
with self.assertLogs("null", "DEBUG") as _:
tr.finalize()
self.assertTrue(tr.is_coding)
b12 = tr.as_bed12()
self.assertEqual(b12.thick_start, tr.combined_cds_end)
self.assertEqual(b12.thick_end, tr.combined_cds_start)
self.assertEqual(len(b12.block_sizes), tr.exon_num)
self.assertEqual(b12.block_sizes,
[200, 200, 400, 500],
b12.block_sizes)
self.assertEqual(b12.strand, "-")
self.assertEqual(b12.block_starts,
[0, 300, 700, 2400],
b12.block_starts)
self.assertEqual(tr.format("bed12"), str(b12))
self.assertEqual(str(b12),
"\t".join([str(_) for _ in
["Chr1", 100, 3000, tr.id, 0, tr.strand,
b12.thick_start - 1, b12.thick_end,
0, 4,
",".join([str(__) for __ in [200, 200, 400, 500]]),
",".join([str(___) for ___ in [0, 300, 700, 2400]])]]
))
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)
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)
def test_add_two_partials(self):
logger = create_null_logger("test_add_two_partials")
logger.setLevel("INFO")
json_conf = load_and_validate_config(None)
json_conf.reference.genome = self.fai
json_conf.pick.alternative_splicing.only_confirmed_introns = False
json_conf.pick.run_options.only_reference_update = True
ref = Transcript(is_reference=True)
ref.chrom, ref.strand, ref.id = "Chr5", "-", "AT5G66670.2"
ref.add_exons([(26611258, 26612889)])
ref.add_exons([(26611474, 26612700)], features=["CDS"])
ref.finalize()
self.assertTrue(ref.is_coding)
# Chr5 TAIR10 mRNA 26611258 26612889 . - . ID=AT5G66670.2;Parent=AT5G66670;Name=AT5G66670.2;index=1
# Chr5 TAIR10 protein 26611474 26612700 . - . ID=AT5G66670.2-Protein;Parent=AT5G66670.2;Name=AT5G66670.2;derives_from=AT5G66670.2
# Chr5 TAIR10 three_prime_UTR 26611258 26611473 . - . Parent=AT5G66670.2
# Chr5 TAIR10 CDS 26611474 26612700 . - 0 Parent=AT5G66670.2
# Chr5 TAIR10 five_prime_UTR 26612701 26612889 . - . Parent=AT5G66670.2
# Chr5 TAIR10 exon 26611258 26612889 . - . Parent=AT5G66670.2
template1 = Transcript(is_reference=False)
template1.chrom, template1.strand, template1.id = ref.chrom, ref.strand, ref.id + "_frag1"
template1.add_exons(((26611116, 26611157), (26611258, 26612670)))
template1.add_exons(((26611474, 26612670), ), features=["CDS"])
template1.finalize()
self.assertTrue(template1.is_coding)
template2 = Transcript(is_reference=False)
template2.chrom, template2.strand, template2.id = ref.chrom, ref.strand, ref.id + "_frag2"
template2.add_exons(((26611574, 26612889), (26613007, 26613403)))
template2.add_exons(((26611574, 26612700), ), features=["CDS"])
template2.finalize()
self.assertTrue(template2.is_coding)
logger.setLevel("INFO")
json_conf.pick.alternative_splicing.pad = True
locus = Locus(ref, configuration=json_conf, logger=logger)
locus.add_transcript_to_locus(template1)
locus.add_transcript_to_locus(template2)
self.assertIn(template2.id, locus)
# self.assertIn(template1.id, locus)
# locus.logger.setLevel("DEBUG")
# for tid in locus:
# locus[tid].logger.setLevel("DEBUG")
locus.finalize_alternative_splicing(check_requirements=False)
self.assertTrue(locus._finalized)
self.assertNotIn(template1.id, locus, "\n" + str(locus))
self.assertNotIn(template2.id, locus, "\n" + str(locus))
self.assertEqual(
locus[ref.id].end, template2.end,
((locus[ref.id].end, ref.end, template2.end, template1.end),
(locus[ref.id].start, ref.start, template2.start,
template1.start)))
class WrongLoadedOrf(unittest.TestCase):
def setUp(self):
self.tr = Transcript()
self.tr.start, self.tr.end, self.tr.chrom, self.tr.strand = (101, 1000,
"Chr1",
"+")
self.tr.id = "test1"
self.tr.add_exons([(101, 400), (701, 1000)])
self.tr.finalize()
def test_load_invalid_length(self):
b_invalid = BED12(transcriptomic=True)
b_invalid.chrom = self.tr.id
self.assertTrue(b_invalid.transcriptomic)
# b_invalid.name = self.tr.id
b_invalid.start = 0
b_invalid.strand = "+"
b_invalid.end = self.tr.cdna_length + 10
b_invalid.thick_start = 101
b_invalid.thick_end = 190
self.assertEqual(b_invalid.chrom, b_invalid.id, b_invalid.id)
with self.assertLogs("null", "WARNING") as cm:
retrieval.load_orfs(self.tr, [b_invalid])
found_message = False
for _ in cm.output:
if "Wrong ORF for {}:".format(self.tr.id) in _:
found_message = True
break
self.assertTrue(found_message, cm.output)
def test_load_invalid_multiple(self):
b_valid = BED12(transcriptomic=True)
b_valid.chrom = self.tr.id
b_valid.name = "valid"
b_valid.start, b_valid.end, b_valid.strand = 0, self.tr.cdna_length - 1, "+"
b_valid.thick_start, b_valid.thick_end = 101, 190
b_invalid = b_valid.copy()
b_invalid.name = "invalid"
b_invalid.thick_start = 1
b_invalid.thick_end = 89
b_invalid.phase = 0
self.assertTrue(b_invalid.invalid)
self.assertFalse(b_valid.invalid, b_valid.invalid_reason)
with self.assertLogs("null", "DEBUG") as _:
retrieval.load_orfs(self.tr, [b_valid, b_invalid])
# print(*cm.output, sep="\n")
self.assertEqual(self.tr.number_internal_orfs, 1)
def test_filter_non_transcriptomic(self):
b_valid = BED12(transcriptomic=True)
b_valid.chrom = self.tr.id
b_valid.name = "valid"
b_valid.start, b_valid.end, b_valid.strand = 0, self.tr.cdna_length - 1, "+"
b_valid.thick_start, b_valid.thick_end = 101, 190
b_invalid = b_valid.copy()
b_invalid.name = "non-transcriptomic"
b_invalid.transcriptomic = False
retained = retrieval.find_overlapping_cds(self.tr,
[b_invalid, b_valid])
self.assertEqual(retained, [b_valid])
class PhaseChecker(unittest.TestCase):
logger = create_default_logger("pcheck")
logger.setLevel("DEBUG")
def setUp(self):
lines = """Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 mRNA 40282 46004 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960;Name=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2;aed=0.0;note=TRIAE_CS42_5DL_TGACv1_434051_AA1427960;confidence=High;has_start=True;has_stop=True;original_stop=True;protein_rank=P1;transcript_rank=T2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 40282 40933 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon1;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 three_prime_UTR 40282 40720 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.three_prime_UTR1;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 40721 40933 . - 0 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS1;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 41018 41111 . - 1 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS2;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 41018 41111 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon2;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 41227 41468 . - 0 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS3;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 41227 41468 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon3;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 41673 41831 . - 0 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS4;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 41673 41831 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon4;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 41946 42820 . - 2 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS5;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 41946 42820 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon5;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 42905 42913 . - 2 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS6;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 42905 42913 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon6;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 45373 45496 . - 0 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS7;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 45373 45496 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon7;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 45600 45651 . - 1 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS8;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 45600 45651 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon8;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 45726 45726 . - 2 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS9;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 45726 45726 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon9;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 CDS 45875 45893 . - 0 ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.CDS10;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 exon 45875 46004 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.exon10;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2
Triticum_aestivum_CS42_TGACv1_scaffold_434051_5DL TGACv1 five_prime_UTR 45894 46004 . - . ID=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2.five_prime_UTR1;Parent=TRIAE_CS42_5DL_TGACv1_434051_AA1427960.2"""
lines = [GffLine("\t".join(_.split())) for _ in lines.split("\n") if _]
self.transcript = Transcript(lines[0], logger=self.logger)
self.transcript.add_exons(lines[1:])
self.correct_phases = {(40721, 40933): 2,
(41018, 41111): 0,
(41227, 41468): 2,
(41673, 41831): 2,
(41946, 42820): 1,
(42905, 42913): 1,
(45373, 45496): 2,
(45600, 45651): 0,
(45726, 45726): 2,
(45875, 45893): 0}
@unittest.skip
def test_check_phases(self):
self.transcript.finalize()
phases = dict((_[1], _[2]) for _ in self.transcript.internal_orfs[0]
if _[0] == "CDS")
self.assertEqual(self.transcript.combined_cds_start, 45893)
self.assertEqual(phases.keys(),
self.correct_phases.keys(),
list(zip(sorted(phases.keys()),
sorted(self.correct_phases.keys()))))
if self.correct_phases != phases:
for key in sorted(phases.keys(), reverse=True):
self.assertEqual(phases[key], self.correct_phases[key],
(key, phases[key], self.correct_phases[key]))
self.assertEqual(self.correct_phases,
phases,
(self.correct_phases, phases))
def test_removal_after_padding(self):
"""Here we test that, given three transcripts, the first one will be expanded to be identical to the second;
the second will be removed as redundant; the third will be expanded to compatible with the padded first.
"""
logger = create_default_logger("test_add_two_partials", "INFO")
json_conf = load_and_validate_config(None)
json_conf.reference.genome = self.fai
json_conf.pick.alternative_splicing.min_cds_overlap = 0.2
json_conf.pick.alternative_splicing.min_cdna_overlap = 0.2
json_conf.pick.alternative_splicing.only_confirmed_introns = False
json_conf.pick.alternative_splicing.keep_retained_introns = True
json_conf.pick.alternative_splicing.pad = True
json_conf.scoring.requirements.expression = ["cdna_length"]
json_conf.scoring.requirements.parameters = {
"cdna_length": SizeFilter(operator="gt", value=0)
}
json_conf.scoring.requirements._expression = json_conf.scoring.requirements._create_expression(
json_conf.scoring.requirements.expression,
json_conf.scoring.requirements.parameters)
json_conf.scoring.as_requirements.expression = ["cdna_length"]
json_conf.scoring.as_requirements.parameters = {
"cdna_length": SizeFilter(operator="gt", value=0)
}
json_conf.scoring.as_requirements._expression = json_conf.scoring.requirements._create_expression(
json_conf.scoring.requirements.expression,
json_conf.scoring.requirements.parameters)
t1 = Transcript(
BED12(
"Chr5\t26584779\t26587869\tID=AT5G66610.1;coding=True;phase=0\t0\t+\t26585222\t26587755\t0\t11\t\
100,54,545,121,78,105,213,63,119,59,443\t0,440,565,1202,1437,1640,1858,2154,2304,2507,2647"
))
t2_1 = Transcript(
BED12(
"Chr5\t26584773\t26586510\tID=AT5G66610.2_1;coding=True;phase=0\t0\t+\t26585222\t26586510\t0\t\
6\t177,54,545,121,78,85\t0,446,571,1208,1443,1652"))
t2_2 = Transcript(
BED12(
"Chr5\t26584873\t26587782\tID=AT5G66610.2_2;coding=True;phase=0\t0\t+\t26585222\t\
26587755\t0\t10\t77,54,545,121,78,99,213,63,119,496\t0,346,471,1108,1343,1552,1764,2060,2210,2413"
))
t1.finalize()
t2_1.finalize()
t2_2.finalize()
t1.is_reference = True
self.assertEqual(t1.start, 26584780)
locus = Locus(t1, logger=logger, configuration=json_conf)
locus.add_transcript_to_locus(t2_1, check_in_locus=False)
locus.add_transcript_to_locus(t2_2, check_in_locus=False)
self.assertTrue(locus.primary_transcript_id == t1.id)
locus.logger.setLevel("INFO")
locus.finalize_alternative_splicing(_scores={
t1.id: 20,
t2_1.id: 15,
t2_2.id: 10
})
self.assertIn(t1.id, locus.transcripts)
if t2_1.id in locus.transcripts:
for tid1, tid2 in itertools.combinations(locus.transcripts.keys(),
2):
res, _ = Assigner.compare(locus[tid1], locus[tid2])
print(tid1, tid2, res.ccode)
self.assertNotIn(t2_1.id, locus.transcripts.keys(),
[(key, val.start, val.end)
for key, val in locus.transcripts.items()])
self.assertIn(t2_2.id, locus.transcripts,
"\n".join(tr.format("bed12") for tr in locus))
self.assertTrue(locus[t2_2.id].attributes["padded"])
# self.assertTrue(locus[t1.id].attributes["padded"])
self.assertGreaterEqual(t1.start, locus[t1.id].start,
locus[t1.id].format("bed12"))
self.assertEqual(
locus[t2_2.id].start,
locus[t1.id].start,
((locus[t2_2.id].start, t1.start, t2_1.start, t2_2.start),
(locus[t2_2.id].end, t1.end, t2_1.end, t2_2.end)),
)
self.assertEqual(locus[t1.id].end, locus[t2_2.id].end)
class TestMetricsEndDistances(unittest.TestCase):
logger = create_default_logger("End")
logger.setLevel("ERROR")
def setUp(self):
self.tr = Transcript()
self.tr.logger = self.logger
self.tr.start = 101
self.tr.end = 10000
self.tr.add_exons([(101, 300),
(501, 800),
(1001, 1200),
(1301, 2000),
(3501, 5000),
(5501, 6000),
(6201, 7000),
(7301, 7700),
(8201, 9000),
(9101, 9300),
(9501, 9700),
(9801, 10000)])
self.tr.id = "test1"
self.tr.parent = "test1.gene"
def test_end_positive(self):
self.tr.strand = "+"
cds = [(1161, 1200), # 40 % 3 == 1
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9130)]
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.selected_cds_end,
9130)
self.assertEqual(self.tr.end_distance_from_junction,
(9300 - 9131 + 1) + (9700 - 9501 + 1)
)
self.assertEqual(self.tr.end_distance_from_tes,
(9300 - 9131 + 1) + (9700 - 9501 + 1) + (10000 - 9801 + 1)
)
self.tr.strip_cds()
self.assertEqual(len(self.tr.internal_orfs), 0, self.tr.internal_orfs)
self.tr.finalized = False
cds = [(1161, 1200), # 40 % 3 == 1
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9300), # 200 % 3 == 2
(9501, 9690) # 190 % 3 == 1
]
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertEqual(self.tr.combined_cds_end,
9690)
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.end_distance_from_junction,
(9700 - 9691 + 1)
)
self.assertEqual(self.tr.end_distance_from_tes,
(9700 - 9691 + 1) + (10000 - 9801 + 1)
)
self.tr.strip_cds()
self.assertEqual(self.tr.combined_cds_end,
self.tr.selected_cds_end,
self.tr.combined_cds)
self.assertEqual(self.tr.combined_cds_end,
None,
self.tr.combined_cds_end)
self.tr.finalized = False
cds = [(1161, 1200), # 40 % 3 == 1
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9300), # 200 % 3 == 2
(9501, 9700), # 200 % 3 == 2
(9801, 9820), # 20 % 2 == 2
]
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertEqual(self.tr.combined_cds_end,
9820)
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.end_distance_from_tes,
180)
self.assertEqual(self.tr.end_distance_from_junction,
0)
def test_end_negative(self):
self.tr.strand = "-"
# self.tr.add_exons([(101, 300),
# (501, 800),
# (1001, 1200),
# (1301, 2000),
# (3501, 5000),
# (5501, 6000),
# (6201, 7000),
# (7301, 7700),
# (8201, 9000),
# (9101, 9300),
# (9501, 9700),
# (9801, 10000)])
cds = [(1161, 1200), # 40 % 3 == 1
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9130)]
self.assertEqual(sum(x[1] - x[0] + 1 for x in cds) % 3, 0)
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertTrue(self.tr.is_coding)
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.selected_cds_end,
1161)
self.assertEqual(self.tr.end_distance_from_junction,
(1161-1001) + (800-501+1),
(self.tr.end_distance_from_junction,
(1161-1001) + (800-501+1))
)
self.assertEqual(self.tr.end_distance_from_tes,
self.tr.end_distance_from_junction + (300 - 101 + 1),
(self.tr.end_distance_from_tes,
self.tr.end_distance_from_junction + (300 - 101 + 1))
)
self.tr.strip_cds()
self.assertEqual(len(self.tr.internal_orfs), 0, self.tr.internal_orfs)
self.tr.finalized = False
cds = [(721, 800),
(1001, 1200), # 200 % 3 == 2
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9130), # 200 % 3 == 2
]
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertEqual(self.tr.combined_cds_end,
721)
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.end_distance_from_junction,
(721-501),
(self.tr.end_distance_from_junction, (721-501))
)
self.assertEqual(self.tr.end_distance_from_tes,
self.tr.end_distance_from_junction + (300 - 101 + 1),
(self.tr.end_distance_from_tes,
self.tr.end_distance_from_junction + (300 - 101 + 1))
)
self.tr.strip_cds()
self.assertEqual(self.tr.combined_cds_end,
self.tr.selected_cds_end,
self.tr.combined_cds)
self.assertEqual(self.tr.combined_cds_end,
None,
self.tr.combined_cds_end)
self.tr.finalized = False
cds = [(161, 300), # 140 % 3 == 2
(501, 800), # 300 % 3 == 0
(1001, 1200), # 200 % 3 == 2
(1301, 2000), # 700 % 3 == 1
(3501, 5000), # 1500 % 3 == 0
(5501, 6000), # 500 % 3 == 2
(6201, 7000), # 800 % 3 == 2
(7301, 7700), # 400 % 3 == 1
(8201, 9000), # 800 % 3 == 2
(9101, 9130), # 30 % 3 == 0
]
self.assertEqual(sum((_[1] - _[0] +1) % 3 for _ in cds ) % 3, 0)
self.tr.logger = self.logger
self.tr.add_exons(cds, features="CDS")
self.tr.finalize()
self.assertEqual(self.tr.combined_cds_end,
161)
self.assertEqual(self.tr.selected_cds_end,
self.tr.combined_cds_end)
self.assertEqual(self.tr.end_distance_from_tes,
60)
self.assertEqual(self.tr.end_distance_from_junction,
0)
class TranscriptTester(unittest.TestCase):
tr_gff = """Chr1 TAIR10 mRNA 5928 8737 . . . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
Chr1 TAIR10 exon 5928 8737 . . . Parent=AT1G01020.1"""
tr_lines = tr_gff.split("\n")
for pos, line in enumerate(tr_lines):
tr_lines[pos] = re.sub("\s+", "\t", line)
assert len(tr_lines[pos].split("\t")) == 9, line.split("\t")
tr_gff_lines = [Mikado.parsers.GFF.GffLine(line) for line in tr_lines]
for l in tr_gff_lines:
assert l.header is False
# print(l)
logger = create_null_logger("null")
def setUp(self):
"""Basic creation test."""
self.tr = Transcript()
self.tr.logger = self.logger
self.tr.chrom = "Chr1"
self.tr.source = "TAIR10"
self.tr.feature = "mRNA"
self.tr.start = 5928
self.tr.end = 8737
self.tr.strand = "+"
self.tr.add_exon((5928, 8737))
self.tr.score = None
self.tr.id, self.tr.parent, self.tr.name = "AT1G01020.1", "AT1G01020", "AT1G01020.1"
self.tr.add_exon((8571, 8666), "CDS")
self.tr.finalize()
self.orf = Mikado.parsers.bed12.BED12()
self.orf.chrom = self.tr.id
self.orf.start = 1
self.orf.end = self.tr.cdna_length
self.orf.name = self.tr.id
self.orf.strand = "+"
self.orf.score = 0
self.orf.thick_start = 8571 - 5928 + 1
self.orf.thick_end = 8666 - 5928 + 1
self.orf.block_count = 1
self.orf.blockSize = self.tr.cdna_length
self.orf.block_starts = 0
self.orf.has_start_codon = True
self.orf.has_stop_codon = True
self.orf.transcriptomic = True
self.assertFalse(self.orf.invalid, self.orf.invalid_reason)
self.assertEqual((self.orf.thick_end - self.orf.thick_start + 1) % 3,
0)
def test_invalid_inizialization(self):
with self.assertRaises(TypeError):
_ = Mikado.loci.Transcript(self.tr_gff_lines[1])
def test_basics(self):
self.assertEqual(self.tr.chrom, "Chr1")
self.assertEqual(self.tr.exon_num, 1)
self.assertEqual(self.tr.monoexonic, True)
self.assertEqual(self.tr.exon_num, len(self.tr.exons))
self.assertEqual(self.tr.start, 5928)
self.assertEqual(self.tr.end, 8737)
self.assertEqual(self.tr.exons, [tuple([5928, 8737])], self.tr.exons)
def test_cds(self):
"""Test the CDS features.
Note that in a single-exon transcript with no strand, start_codon and stop_codon are defined as False.
"""
self.tr.load_orfs([self.orf])
self.assertEqual(self.tr.combined_cds, self.tr.selected_cds)
self.assertEqual(self.tr.combined_cds, [tuple([8571, 8666])],
self.tr.combined_cds)
self.assertEqual(self.tr.selected_cds_start, 8571)
self.assertEqual(self.tr.selected_cds_end, 8666)
self.assertEqual(self.tr.has_start_codon, True)
self.assertEqual(self.tr.has_stop_codon, True)
def test_equality(self):
new_transcript = self.tr.deepcopy()
self.assertTrue(new_transcript == self.tr)
new_transcript.strand = None
self.assertFalse(
new_transcript == self.tr) # They have now a different strand
new_transcript.unfinalize()
new_transcript.strand = "+" # It becomes a multiexonic transcript, so it must have a strand
new_transcript.end = 9737
new_exon = Mikado.parsers.GFF.GffLine(self.tr_lines[-1])
new_exon.strand = "+"
new_exon.start = 9000
new_exon.end = 9737
new_transcript.add_exon(new_exon)
new_transcript.finalize()
self.assertTrue(new_transcript != self.tr)
def test_mono_finalising(self):
transcript_line = [
line for line in self.tr_gff_lines if line.feature == "mRNA"
]
self.assertEqual(len(transcript_line), 1,
"\n".join([str(line) for line in self.tr_gff_lines]))
tr = Mikado.loci.Transcript(transcript_line[0])
exon_lines = [
line for line in self.tr_gff_lines
if line.is_exon is True and "UTR" not in line.feature.upper()
]
tr.add_exons(exon_lines)
tr.add_exon((8571, 8666), "CDS")
tr.finalize()
self.assertGreater(tr.three_utr_length, 0)
self.assertGreater(tr.five_utr_length, 0)
def test_invalid_transcript(self):
lines = """Chr1\tTAIR10\tmRNA\t5928\t8737\t.\t.\t.\tID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
Chr1\tTAIR10\tCDS\t8571\t7500\t.\t.\t0\tParent=AT1G01020.1;
Chr1\tTAIR10\tCDS\t7503\t8666\t.\t.\t0\tParent=AT1G01020.1;
Chr1\tTAIR10\texon\t5928\t8737\t.\t.\t.\tParent=AT1G01020.1"""
gff_lines = [
Mikado.parsers.GFF.GffLine(line) for line in lines.split("\n")
]
self.assertIsInstance(gff_lines[0], Mikado.parsers.GFF.GffLine)
checker = False
if gff_lines[0].feature.endswith(
"transcript") or "RNA" in gff_lines[0].feature.upper():
checker = True
self.assertTrue(checker)
self.assertTrue(gff_lines[0].is_transcript)
transcript = Mikado.loci.Transcript(gff_lines[0])
transcript.logger = self.logger
transcript.add_exons(gff_lines[1:])
with self.assertRaises(Mikado.exceptions.InvalidCDS):
Mikado.loci.transcript_methods.finalizing._check_cdna_vs_utr(
transcript)
def test_utr(self):
self.assertEqual(
self.tr.selected_internal_orf, [("UTR", tuple([5928, 8570])),
("exon", tuple([5928, 8737])),
("CDS", tuple([8571, 8666]), 0),
("UTR", tuple([8667, 8737]))],
"Right: {0}\nFound{1}".format([("UTR", 5928, 8570),
("CDS", 8571, 8666),
("UTR", 8667, 8737)],
self.tr.selected_internal_orf))
self.assertEqual(
self.tr.combined_utr,
[tuple([5928, 8570]), tuple([8667, 8737])])
self.assertEqual(self.tr.five_utr, [tuple([5928, 8570])],
self.tr.five_utr)
self.assertEqual(self.tr.three_utr, [tuple([8667, 8737])])
def test_utr_metrics(self):
"""Test for UTR exon num, start distance, etc."""
self.assertEqual(self.tr.five_utr_num, 1)
self.assertEqual(self.tr.three_utr_num, 1)
self.assertEqual(self.tr.five_utr_length, 8570 + 1 - 5928)
self.assertEqual(self.tr.three_utr_length, 8737 + 1 - 8667)
self.assertEqual(self.tr.selected_start_distance_from_tss, 8571 - 5928,
self.tr.selected_end_distance_from_tes)
self.assertEqual(
self.tr.selected_end_distance_from_tes, 8737 - 8666,
(self.tr.selected_end_distance_from_tes, self.tr.strand))
def test_strip_cds(self):
self.tr.strip_cds()
self.assertEqual(self.tr.selected_cds_length, 0)
self.assertEqual(self.tr.three_utr, [])
self.assertEqual(self.tr.five_utr, [])
self.assertEqual(self.tr.selected_cds, [])
self.assertEqual(self.tr.selected_cds_start, None)
self.assertEqual(self.tr.selected_cds_end, None)
def test_remove_utr(self):
"""Test for CDS stripping. We remove the UTRs and verify that start/end have moved, no UTR is present, etc.
"""
self.tr.remove_utrs()
self.assertEqual(self.tr.selected_cds_start, self.tr.start)
self.assertEqual(self.tr.selected_cds_end, self.tr.end)
self.assertEqual(self.tr.three_utr, [])
self.assertEqual(self.tr.five_utr, [])
self.assertEqual(self.tr.combined_cds, [tuple([8571, 8666])],
self.tr.combined_cds)
self.assertEqual(self.tr.combined_utr, [], self.tr.combined_utr)
def test_negative_orf(self):
"""Test loading a negative strand ORF onto a monoexonic transcript.
This should reverse the ORF."""
self.orf.strand = "-"
self.tr.strip_cds(strand_specific=False)
self.orf.has_stop_codon = False
self.tr.load_orfs([self.orf])
self.assertEqual(self.tr.strand, "-")
self.assertEqual(self.tr.selected_cds_start, 8666)
self.assertEqual(self.tr.selected_cds_end, 8571)
def test_introns(self):
self.assertEqual(self.tr.introns, set([]), self.tr.introns)
self.assertEqual(self.tr.combined_cds_introns, set([]),
self.tr.combined_cds_introns)
self.assertEqual(self.tr.selected_cds_introns, set([]),
self.tr.selected_cds_introns)
def testDoubleOrf(self):
"""Test to verify the introduction of multiple ORFs."""
self.tr.strip_cds()
self.tr.finalized = False
first_orf = Mikado.parsers.bed12.BED12()
first_orf.chrom = self.tr.id
first_orf.start = 1
first_orf.end = self.tr.cdna_length
first_orf.name = self.tr.id
first_orf.strand = "+"
first_orf.score = 0
first_orf.thick_start = 51
first_orf.thick_end = 398
first_orf.block_count = 1
first_orf.blockSize = self.tr.cdna_length
first_orf.block_sizes = [self.tr.cdna_length]
first_orf.block_starts = [0]
first_orf.rgb = 0
first_orf.has_start_codon = True
first_orf.has_stop_codon = True
first_orf.transcriptomic = True
self.assertFalse(first_orf.invalid)
# This should not be incorporated
second_orf = Mikado.parsers.bed12.BED12()
second_orf.chrom = self.tr.id
second_orf.start = 1
second_orf.end = self.tr.cdna_length
second_orf.name = "second"
second_orf.strand = "+"
second_orf.score = 0
second_orf.thick_start = 201
second_orf.thick_end = 410
second_orf.block_count = 1
second_orf.blockSize = self.tr.cdna_length
second_orf.block_sizes = [self.tr.cdna_length]
second_orf.block_starts = [0]
second_orf.rgb = 0
second_orf.has_start_codon = True
second_orf.has_stop_codon = True
second_orf.transcriptomic = True
self.assertFalse(second_orf.invalid)
self.assertTrue(
Mikado.loci.Transcript.is_overlapping_cds(first_orf, second_orf))
# This should be added
third_orf = Mikado.parsers.bed12.BED12()
third_orf.chrom = self.tr.id
third_orf.start = 1
third_orf.end = self.tr.cdna_length
third_orf.name = "third"
third_orf.strand = "+"
third_orf.score = 0
third_orf.thick_start = 501
third_orf.thick_end = 800
third_orf.block_count = 1
third_orf.blockSize = self.tr.cdna_length
third_orf.block_sizes = [self.tr.cdna_length]
third_orf.block_starts = [0]
third_orf.rgb = 0
third_orf.has_start_codon = True
third_orf.has_stop_codon = True
third_orf.transcriptomic = True
self.assertFalse(third_orf.invalid)
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(first_orf, third_orf))
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(second_orf, third_orf))
self.assertFalse(third_orf == second_orf)
self.assertFalse(first_orf == second_orf)
self.assertFalse(first_orf == third_orf)
candidates = [first_orf, second_orf, third_orf]
self.tr.logger = self.logger
self.tr.load_orfs([first_orf])
self.tr.load_orfs([second_orf])
self.tr.load_orfs([third_orf])
self.tr.load_orfs([first_orf, second_orf, third_orf])
self.assertTrue(self.tr.is_complete)
self.tr.finalize()
self.assertEqual(
self.tr.number_internal_orfs, 2,
(self.tr.cdna_length, self.tr.selected_start_distance_from_tss,
self.tr.selected_end_distance_from_tes))
self.assertEqual(self.tr.combined_cds_length, 648)
self.assertEqual(self.tr.selected_cds_length, 348)
self.assertEqual(self.tr.number_internal_orfs, 2,
"\n".join([str(x) for x in self.tr.internal_orfs]))
new_transcripts = sorted(self.tr.split_by_cds())
self.assertEqual(len(new_transcripts), 2)
self.assertEqual(new_transcripts[0].three_utr_length, 0)
self.assertEqual(new_transcripts[1].five_utr_length, 0)
def testDoubleOrf_negative(self):
"""Test to verify the introduction of multiple ORFs."""
self.tr.strip_cds(strand_specific=False)
self.tr.finalized = False
first_orf = Mikado.parsers.bed12.BED12()
first_orf.chrom = self.tr.id
first_orf.start = 1
first_orf.end = self.tr.cdna_length
first_orf.name = self.tr.id
first_orf.strand = "-"
first_orf.score = 0
first_orf.thick_start = 51
first_orf.thick_end = 398
first_orf.block_count = 1
first_orf.blockSize = self.tr.cdna_length
first_orf.block_sizes = [self.tr.cdna_length]
first_orf.block_starts = [0]
first_orf.rgb = 0
first_orf.has_start_codon = True
first_orf.has_stop_codon = True
first_orf.transcriptomic = True
self.assertFalse(first_orf.invalid)
# This should not be incorporated
second_orf = Mikado.parsers.bed12.BED12()
second_orf.chrom = self.tr.id
second_orf.start = 1
second_orf.end = self.tr.cdna_length
second_orf.name = "second"
second_orf.strand = "-"
second_orf.score = 0
second_orf.thick_start = 201
second_orf.thick_end = 410
second_orf.block_count = 1
second_orf.blockSize = self.tr.cdna_length
second_orf.block_sizes = [self.tr.cdna_length]
second_orf.block_starts = [0]
second_orf.rgb = 0
second_orf.has_start_codon = True
second_orf.has_stop_codon = True
second_orf.transcriptomic = True
self.assertFalse(second_orf.invalid)
# self.assertTrue(Mikado.loci.Transcript.is_overlapping_cds(first_orf,
# second_orf))
# This should be added
third_orf = Mikado.parsers.bed12.BED12()
third_orf.chrom = self.tr.id
third_orf.start = 1
third_orf.end = self.tr.cdna_length
third_orf.name = "third"
third_orf.strand = "-"
third_orf.score = 0
third_orf.thick_start = 501
third_orf.thick_end = 800
third_orf.block_count = 1
third_orf.blockSize = self.tr.cdna_length
third_orf.block_sizes = [self.tr.cdna_length]
third_orf.block_starts = [0]
third_orf.rgb = 0
third_orf.has_start_codon = True
third_orf.has_stop_codon = True
third_orf.transcriptomic = True
self.assertFalse(third_orf.invalid)
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(first_orf, third_orf))
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(second_orf, third_orf))
self.assertFalse(third_orf == second_orf)
self.assertFalse(first_orf == second_orf)
self.assertFalse(first_orf == third_orf)
candidates = [first_orf, second_orf, third_orf]
# self.assertEqual(len(self.tr.find_overlapping_cds(candidates)), 2)
self.tr.logger = self.logger
self.tr.load_orfs(candidates)
self.assertTrue(self.tr.is_complete)
self.tr.finalize()
self.assertEqual(
self.tr.number_internal_orfs, 2,
(self.tr.cdna_length, self.tr.selected_start_distance_from_tss,
self.tr.selected_end_distance_from_tes))
# self.assertEqual(self.tr.combined_cds_length, 648)
self.assertEqual(self.tr.selected_cds_length, 348)
self.assertEqual(self.tr.number_internal_orfs, 2,
"\n".join([str(x) for x in self.tr.internal_orfs]))
new_transcripts = sorted(self.tr.split_by_cds())
self.assertEqual(len(new_transcripts), 2)
self.assertEqual(new_transcripts[0].five_utr_length, 0)
self.assertEqual(new_transcripts[1].three_utr_length, 0)
def test_wrong_orf(self):
# This should be added
orf = Mikado.parsers.bed12.BED12()
orf.chrom = self.tr.id
orf.start = 1
orf.end = self.tr.cdna_length + 1
orf.name = "third"
orf.strand = "-"
orf.score = 0
orf.thick_start = 501
orf.thick_end = 800
orf.block_count = 1
orf.blockSize = self.tr.cdna_length
orf.block_sizes = [self.tr.cdna_length]
orf.block_starts = [0]
orf.rgb = 0
orf.has_start_codon = True
orf.has_stop_codon = True
orf.transcriptomic = True
self.assertFalse(orf.invalid)
self.tr.logger = self.logger
self.tr.strip_cds()
self.tr.strand = "+"
self.logger.setLevel("WARNING")
# self.tr.load_orfs([orf])
with self.assertLogs("null", level="DEBUG") as cm_out:
self.tr.load_orfs([orf])
self.assertFalse(self.tr.is_coding)
class TranscriptTester(unittest.TestCase):
tr_gff = """Chr1 TAIR10 mRNA 5928 8737 . . . ID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
Chr1 TAIR10 exon 5928 8737 . . . Parent=AT1G01020.1"""
tr_lines = tr_gff.split("\n")
for pos, line in enumerate(tr_lines):
tr_lines[pos] = re.sub("\s+", "\t", line)
assert len(tr_lines[pos].split("\t")) == 9, line.split("\t")
tr_gff_lines = [Mikado.parsers.GFF.GffLine(line) for line in tr_lines]
for l in tr_gff_lines:
assert l.header is False
# print(l)
logger = create_null_logger("null")
def setUp(self):
"""Basic creation test."""
self.tr = Transcript()
self.tr.logger = self.logger
self.tr.chrom = "Chr1"
self.tr.source = "TAIR10"
self.tr.feature = "mRNA"
self.tr.start = 5928
self.tr.end = 8737
self.tr.strand = "+"
self.tr.add_exon((5928, 8737))
self.tr.score = None
self.tr.id, self.tr.parent, self.tr.name = "AT1G01020.1", "AT1G01020", "AT1G01020.1"
self.tr.add_exon((8571, 8666), "CDS")
self.tr.finalize()
self.orf = Mikado.parsers.bed12.BED12()
self.orf.chrom = self.tr.id
self.orf.start = 1
self.orf.end = self.tr.cdna_length
self.orf.name = self.tr.id
self.orf.strand = "+"
self.orf.score = 0
self.orf.thick_start = 8571 - 5928 + 1
self.orf.thick_end = 8666 - 5928 + 1
self.orf.block_count = 1
self.orf.blockSize = self.tr.cdna_length
self.orf.block_starts = 0
self.orf.has_start_codon = True
self.orf.has_stop_codon = True
self.orf.transcriptomic = True
self.assertFalse(self.orf.invalid, self.orf.invalid_reason)
self.assertEqual((self.orf.thick_end - self.orf.thick_start + 1) % 3, 0)
def test_invalid_inizialization(self):
with self.assertRaises(TypeError):
_ = Mikado.loci.Transcript(self.tr_gff_lines[1])
def test_basics(self):
self.assertEqual(self.tr.chrom, "Chr1")
self.assertEqual(self.tr.exon_num, 1)
self.assertEqual(self.tr.monoexonic, True)
self.assertEqual(self.tr.exon_num, len(self.tr.exons))
self.assertEqual(self.tr.start, 5928)
self.assertEqual(self.tr.end, 8737)
self.assertEqual(self.tr.exons,
[tuple([5928, 8737])],
self.tr.exons)
def test_cds(self):
"""Test the CDS features.
Note that in a single-exon transcript with no strand, start_codon and stop_codon are defined as False.
"""
self.tr.load_orfs([self.orf])
self.assertEqual(self.tr.combined_cds, self.tr.selected_cds)
self.assertEqual(self.tr.combined_cds,
[tuple([8571, 8666])],
self.tr.combined_cds)
self.assertEqual(self.tr.selected_cds_start, 8571)
self.assertEqual(self.tr.selected_cds_end, 8666)
self.assertEqual(self.tr.has_start_codon, True)
self.assertEqual(self.tr.has_stop_codon, True)
def test_equality(self):
new_transcript = self.tr.deepcopy()
self.assertTrue(new_transcript == self.tr)
new_transcript.strand = None
self.assertFalse(new_transcript == self.tr) # They have now a different strand
new_transcript.unfinalize()
new_transcript.strand = "+" # It becomes a multiexonic transcript, so it must have a strand
new_transcript.end = 9737
new_exon = Mikado.parsers.GFF.GffLine(self.tr_lines[-1])
new_exon.strand = "+"
new_exon.start = 9000
new_exon.end = 9737
new_transcript.add_exon(new_exon)
new_transcript.finalize()
self.assertTrue(new_transcript != self.tr)
def test_mono_finalising(self):
transcript_line = [line for line in self.tr_gff_lines if line.feature == "mRNA" ]
self.assertEqual(len(transcript_line), 1,
"\n".join([str(line) for line in self.tr_gff_lines]))
tr = Mikado.loci.Transcript(transcript_line[0])
exon_lines = [line for line in self.tr_gff_lines if
line.is_exon is True and "UTR" not in line.feature.upper()]
tr.add_exons(exon_lines)
tr.add_exon((8571, 8666), "CDS")
tr.finalize()
self.assertGreater(tr.three_utr_length, 0)
self.assertGreater(tr.five_utr_length, 0)
def test_invalid_transcript(self):
lines = """Chr1\tTAIR10\tmRNA\t5928\t8737\t.\t.\t.\tID=AT1G01020.1;Parent=AT1G01020;Name=AT1G01020.1;Index=1
Chr1\tTAIR10\tCDS\t8571\t7500\t.\t.\t0\tParent=AT1G01020.1;
Chr1\tTAIR10\tCDS\t7503\t8666\t.\t.\t0\tParent=AT1G01020.1;
Chr1\tTAIR10\texon\t5928\t8737\t.\t.\t.\tParent=AT1G01020.1"""
gff_lines = [Mikado.parsers.GFF.GffLine(line) for line in lines.split("\n")]
self.assertIsInstance(gff_lines[0], Mikado.parsers.GFF.GffLine)
checker = False
if gff_lines[0].feature.endswith("transcript") or "RNA" in gff_lines[0].feature.upper():
checker = True
self.assertTrue(checker)
self.assertTrue(gff_lines[0].is_transcript)
transcript = Mikado.loci.Transcript(gff_lines[0])
transcript.logger = self.logger
transcript.add_exons(gff_lines[1:])
with self.assertRaises(Mikado.exceptions.InvalidCDS):
Mikado.transcripts.transcript_methods.finalizing._check_cdna_vs_utr(transcript)
def test_utr(self):
self.assertEqual(self.tr.selected_internal_orf,
[("UTR", tuple([5928, 8570])),
("exon", tuple([5928, 8737])),
("CDS", tuple([8571, 8666]), 0),
("UTR", tuple([8667, 8737]))],
"Right: {0}\nFound{1}".format([("UTR", 5928, 8570), ("CDS", 8571, 8666), ("UTR", 8667, 8737)],
self.tr.selected_internal_orf))
self.assertEqual(self.tr.combined_utr, [tuple([5928, 8570]),
tuple([8667, 8737])])
self.assertEqual(self.tr.five_utr, [tuple([5928, 8570])],
self.tr.five_utr)
self.assertEqual(self.tr.three_utr, [tuple([8667, 8737])])
def test_utr_metrics(self):
"""Test for UTR exon num, start distance, etc."""
self.assertEqual(self.tr.five_utr_num, 1)
self.assertEqual(self.tr.three_utr_num, 1)
self.assertEqual(self.tr.five_utr_length, 8570 + 1 - 5928)
self.assertEqual(self.tr.three_utr_length, 8737 + 1 - 8667)
self.assertEqual(self.tr.selected_start_distance_from_tss,
8571 - 5928,
self.tr.selected_end_distance_from_tes)
self.assertEqual(self.tr.selected_end_distance_from_tes,
8737 - 8666,
(self.tr.selected_end_distance_from_tes, self.tr.strand))
def test_strip_cds(self):
self.tr.strip_cds()
self.assertEqual(self.tr.selected_cds_length, 0)
self.assertEqual(self.tr.three_utr, [])
self.assertEqual(self.tr.five_utr, [])
self.assertEqual(self.tr.selected_cds, [])
self.assertEqual(self.tr.selected_cds_start, None)
self.assertEqual(self.tr.selected_cds_end, None)
def test_remove_utr(self):
"""Test for CDS stripping. We remove the UTRs and verify that start/end have moved, no UTR is present, etc.
"""
self.tr.remove_utrs()
self.assertEqual(self.tr.selected_cds_start, self.tr.start)
self.assertEqual(self.tr.selected_cds_end, self.tr.end)
self.assertEqual(self.tr.three_utr, [])
self.assertEqual(self.tr.five_utr, [])
self.assertEqual(self.tr.combined_cds,
[tuple([8571, 8666])],
self.tr.combined_cds)
self.assertEqual(self.tr.combined_utr, [], self.tr.combined_utr)
def test_negative_orf(self):
"""Test loading a negative strand ORF onto a monoexonic transcript.
This should reverse the ORF."""
self.orf.strand = "-"
self.tr.strip_cds(strand_specific=False)
self.orf.has_stop_codon = False
self.tr.load_orfs([self.orf])
self.assertEqual(self.tr.strand, "-")
self.assertEqual(self.tr.selected_cds_start, 8666)
self.assertEqual(self.tr.selected_cds_end, 8571)
def test_introns(self):
self.assertEqual(self.tr.introns,
set([
]),
self.tr.introns
)
self.assertEqual(self.tr.combined_cds_introns,
set([
]),
self.tr.combined_cds_introns
)
self.assertEqual(self.tr.selected_cds_introns,
set([
]),
self.tr.selected_cds_introns
)
def testDoubleOrf(self):
"""Test to verify the introduction of multiple ORFs."""
self.tr.strip_cds()
self.tr.finalized = False
first_orf = Mikado.parsers.bed12.BED12()
first_orf.chrom = self.tr.id
first_orf.start = 1
first_orf.end = self.tr.cdna_length
first_orf.name = self.tr.id
first_orf.strand = "+"
first_orf.score = 0
first_orf.thick_start = 51
first_orf.thick_end = 398
first_orf.block_count = 1
first_orf.blockSize = self.tr.cdna_length
first_orf.block_sizes = [self.tr.cdna_length]
first_orf.block_starts = [0]
first_orf.rgb = 0
first_orf.has_start_codon = True
first_orf.has_stop_codon = True
first_orf.transcriptomic = True
self.assertFalse(first_orf.invalid)
# This should not be incorporated
second_orf = Mikado.parsers.bed12.BED12()
second_orf.chrom = self.tr.id
second_orf.start = 1
second_orf.end = self.tr.cdna_length
second_orf.name = "second"
second_orf.strand = "+"
second_orf.score = 0
second_orf.thick_start = 201
second_orf.thick_end = 410
second_orf.block_count = 1
second_orf.blockSize = self.tr.cdna_length
second_orf.block_sizes = [self.tr.cdna_length]
second_orf.block_starts = [0]
second_orf.rgb = 0
second_orf.has_start_codon = True
second_orf.has_stop_codon = True
second_orf.transcriptomic = True
self.assertFalse(second_orf.invalid)
self.assertTrue(Mikado.loci.Transcript.is_overlapping_cds(
first_orf, second_orf))
# This should be added
third_orf = Mikado.parsers.bed12.BED12()
third_orf.chrom = self.tr.id
third_orf.start = 1
third_orf.end = self.tr.cdna_length
third_orf.name = "third"
third_orf.strand = "+"
third_orf.score = 0
third_orf.thick_start = 501
third_orf.thick_end = 800
third_orf.block_count = 1
third_orf.blockSize = self.tr.cdna_length
third_orf.block_sizes = [self.tr.cdna_length]
third_orf.block_starts = [0]
third_orf.rgb = 0
third_orf.has_start_codon = True
third_orf.has_stop_codon = True
third_orf.transcriptomic = True
self.assertFalse(third_orf.invalid)
self.assertFalse(Mikado.loci.Transcript.is_overlapping_cds(first_orf, third_orf))
self.assertFalse(Mikado.loci.Transcript.is_overlapping_cds(second_orf, third_orf))
self.assertFalse(third_orf == second_orf)
self.assertFalse(first_orf == second_orf)
self.assertFalse(first_orf == third_orf)
candidates = [first_orf, second_orf, third_orf]
self.tr.logger = self.logger
self.tr.load_orfs([first_orf])
self.tr.load_orfs([second_orf])
self.tr.load_orfs([third_orf])
self.tr.load_orfs([first_orf, second_orf, third_orf])
self.assertTrue(self.tr.is_complete)
self.tr.finalize()
self.assertEqual(self.tr.number_internal_orfs, 2,
(self.tr.cdna_length, self.tr.selected_start_distance_from_tss,
self.tr.selected_end_distance_from_tes))
self.assertEqual(self.tr.combined_cds_length, 648)
self.assertEqual(self.tr.selected_cds_length, 348)
self.assertEqual(self.tr.number_internal_orfs, 2,
"\n".join([str(x) for x in self.tr.internal_orfs]))
new_transcripts = sorted(self.tr.split_by_cds())
self.assertEqual(len(new_transcripts), 2)
self.assertEqual(new_transcripts[0].three_utr_length, 0)
self.assertEqual(new_transcripts[1].five_utr_length, 0)
def testDoubleOrf_negative(self):
"""Test to verify the introduction of multiple ORFs."""
self.tr.strip_cds(strand_specific=False)
self.tr.finalized = False
first_orf = Mikado.parsers.bed12.BED12()
first_orf.chrom = self.tr.id
first_orf.start = 1
first_orf.end = self.tr.cdna_length
first_orf.name = self.tr.id
first_orf.strand = "-"
first_orf.score = 0
first_orf.thick_start = 51
first_orf.thick_end = 398
first_orf.block_count = 1
first_orf.blockSize = self.tr.cdna_length
first_orf.block_sizes = [self.tr.cdna_length]
first_orf.block_starts = [0]
first_orf.rgb = 0
first_orf.has_start_codon = True
first_orf.has_stop_codon = True
first_orf.transcriptomic = True
self.assertFalse(first_orf.invalid)
# This should not be incorporated
second_orf = Mikado.parsers.bed12.BED12()
second_orf.chrom = self.tr.id
second_orf.start = 1
second_orf.end = self.tr.cdna_length
second_orf.name = "second"
second_orf.strand = "-"
second_orf.score = 0
second_orf.thick_start = 201
second_orf.thick_end = 410
second_orf.block_count = 1
second_orf.blockSize = self.tr.cdna_length
second_orf.block_sizes = [self.tr.cdna_length]
second_orf.block_starts = [0]
second_orf.rgb = 0
second_orf.has_start_codon = True
second_orf.has_stop_codon = True
second_orf.transcriptomic = True
self.assertFalse(second_orf.invalid)
# self.assertTrue(Mikado.loci.Transcript.is_overlapping_cds(first_orf,
# second_orf))
# This should be added
third_orf = Mikado.parsers.bed12.BED12()
third_orf.chrom = self.tr.id
third_orf.start = 1
third_orf.end = self.tr.cdna_length
third_orf.name = "third"
third_orf.strand = "-"
third_orf.score = 0
third_orf.thick_start = 501
third_orf.thick_end = 800
third_orf.block_count = 1
third_orf.blockSize = self.tr.cdna_length
third_orf.block_sizes = [self.tr.cdna_length]
third_orf.block_starts = [0]
third_orf.rgb = 0
third_orf.has_start_codon = True
third_orf.has_stop_codon = True
third_orf.transcriptomic = True
self.assertFalse(third_orf.invalid)
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(
first_orf, third_orf))
self.assertFalse(
Mikado.loci.Transcript.is_overlapping_cds(
second_orf, third_orf))
self.assertFalse(third_orf == second_orf)
self.assertFalse(first_orf == second_orf)
self.assertFalse(first_orf == third_orf)
candidates = [first_orf, second_orf, third_orf]
# self.assertEqual(len(self.tr.find_overlapping_cds(candidates)), 2)
self.tr.logger = self.logger
self.tr.load_orfs(candidates)
self.assertTrue(self.tr.is_complete)
self.tr.finalize()
self.assertEqual(self.tr.number_internal_orfs, 2, (
self.tr.cdna_length,
self.tr.selected_start_distance_from_tss,
self.tr.selected_end_distance_from_tes))
# self.assertEqual(self.tr.combined_cds_length, 648)
self.assertEqual(self.tr.selected_cds_length, 348)
self.assertEqual(self.tr.number_internal_orfs, 2, "\n".join([str(x) for x in self.tr.internal_orfs]))
new_transcripts = sorted(self.tr.split_by_cds())
self.assertEqual(len(new_transcripts), 2)
self.assertEqual(new_transcripts[0].five_utr_length, 0)
self.assertEqual(new_transcripts[1].three_utr_length, 0)
def test_wrong_orf(self):
# This should be added
orf = Mikado.parsers.bed12.BED12()
orf.chrom = self.tr.id
orf.start = 1
orf.end = self.tr.cdna_length + 1
orf.name = "third"
orf.strand = "-"
orf.score = 0
orf.thick_start = 501
orf.thick_end = 800
orf.block_count = 1
orf.blockSize = self.tr.cdna_length
orf.block_sizes = [self.tr.cdna_length]
orf.block_starts = [0]
orf.rgb = 0
orf.has_start_codon = True
orf.has_stop_codon = True
orf.transcriptomic = True
self.assertFalse(orf.invalid)
self.tr.logger = self.logger
self.tr.strip_cds()
self.tr.strand = "+"
self.logger.setLevel("WARNING")
# self.tr.load_orfs([orf])
with self.assertLogs("null", level="DEBUG") as cm_out:
self.tr.load_orfs([orf])
self.assertFalse(self.tr.is_coding)
class WrongLoadedOrf(unittest.TestCase):
def setUp(self):
self.tr = Transcript()
self.tr.start, self.tr.end, self.tr.chrom, self.tr.strand = (101, 1000, "Chr1", "+")
self.tr.id = "test1"
self.tr.add_exons([(101, 400), (701, 1000)])
self.tr.finalize()
def test_load_invalid_length(self):
b_invalid = BED12(transcriptomic=True)
b_invalid.chrom = self.tr.id
self.assertTrue(b_invalid.transcriptomic)
# b_invalid.name = self.tr.id
b_invalid.start = 0
b_invalid.strand = "+"
b_invalid.end = self.tr.cdna_length + 10
b_invalid.thick_start = 101
b_invalid.thick_end = 190
self.assertEqual(b_invalid.chrom,
b_invalid.id,
b_invalid.id)
with self.assertLogs("null", "WARNING") as cm:
retrieval.load_orfs(self.tr, [b_invalid])
found_message = False
for _ in cm.output:
if "Wrong ORF for {}:".format(self.tr.id) in _:
found_message = True
break
self.assertTrue(found_message, cm.output)
def test_load_invalid_multiple(self):
b_valid = BED12(transcriptomic=True)
b_valid.chrom = self.tr.id
b_valid.name = "valid"
b_valid.start, b_valid.end, b_valid.strand = 0, self.tr.cdna_length - 1, "+"
b_valid.thick_start, b_valid.thick_end = 101, 190
b_invalid = b_valid.copy()
b_invalid.name = "invalid"
b_invalid.thick_start = 1
b_invalid.thick_end = 89
b_invalid.phase = 0
self.assertTrue(b_invalid.invalid)
self.assertFalse(b_valid.invalid, b_valid.invalid_reason)
with self.assertLogs("null", "DEBUG") as _:
retrieval.load_orfs(self.tr, [b_valid, b_invalid])
# print(*cm.output, sep="\n")
self.assertEqual(self.tr.number_internal_orfs, 1)
def test_filter_non_transcriptomic(self):
b_valid = BED12(transcriptomic=True)
b_valid.chrom = self.tr.id
b_valid.name = "valid"
b_valid.start, b_valid.end, b_valid.strand = 0, self.tr.cdna_length - 1, "+"
b_valid.thick_start, b_valid.thick_end = 101, 190
b_invalid = b_valid.copy()
b_invalid.name = "non-transcriptomic"
b_invalid.transcriptomic = False
retained = retrieval.find_overlapping_cds(self.tr, [b_invalid, b_valid])
self.assertEqual(retained, [b_valid])