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)
class ExternalTester(unittest.TestCase):
def setUp(self):
self.transcript = Transcript()
self.transcript.chrom = "15"
self.transcript.source = "protein_coding"
self.transcript.start = 47631264
self.transcript.end = 48051999
exons = [(47631264, 47631416), (47704590, 47704669),
(47762671, 47762742), (47893062, 47893093),
(47895572, 47895655), (48051942, 48051999)]
self.transcript.strand = "+"
self.transcript.add_exons(exons)
self.transcript.id = "ENST00000560636"
self.transcript.parent = "ENSG00000137872"
def test_copying(self):
self.transcript.external_scores.update({"test": 0, "test1": 1})
self.assertEqual(self.transcript.external_scores.test, 0)
self.assertEqual(self.transcript.external_scores.test1, 1)
transcript = self.transcript.deepcopy()
self.assertEqual(transcript.external_scores.test, 0)
self.assertEqual(transcript.external_scores.test1, 1)
class ExternalTester(unittest.TestCase):
def setUp(self):
self.transcript = Transcript()
self.transcript.chrom = "15"
self.transcript.source = "protein_coding"
self.transcript.start = 47631264
self.transcript.end = 48051999
exons = [(47631264, 47631416),
(47704590, 47704669),
(47762671, 47762742),
(47893062, 47893093),
(47895572, 47895655),
(48051942, 48051999)]
self.transcript.strand = "+"
self.transcript.add_exons(exons)
self.transcript.id = "ENST00000560636"
self.transcript.parent = "ENSG00000137872"
def test_copying(self):
self.transcript.external_scores.update({"test": 0, "test1": 1})
self.assertEqual(self.transcript.external_scores.test, 0)
self.assertEqual(self.transcript.external_scores.test1, 1)
transcript = self.transcript.deepcopy()
self.assertEqual(transcript.external_scores.test, 0)
self.assertEqual(transcript.external_scores.test1, 1)
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)
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 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 TestPadding(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.fai = pkg_resources.resource_filename("Mikado.tests",
"chr5.fas.gz")
def setUp(self):
self.reference = "Chr5\t26574999\t26578625\tID=AT5G66600.3;coding=True;phase=0\t0\t-\t26575104\t26578315\t0\t11\t411,126,87,60,100,809,126,72,82,188,107\t0,495,711,885,1035,1261,2163,2378,2856,3239,3519"
self.reference = Transcript(BED12(self.reference),
source="TAIR10",
is_reference=True)
def test_basic_padding(self):
logger = create_null_logger("test_basic_padding")
logger.setLevel("INFO")
template = self.reference.copy()
template.id = "AT5G66600.3_exp"
template.strip_cds()
template.unfinalize()
template.remove_exon((26575000, 26575410)) # First exon
template.start = 26574650
template.add_exon((26574970, 26575410)) # New exon, template at 5'
template.add_exon((26574650, 26574820)) # New UTR exon
template.remove_exon((26578519, 26578625)) # Last exon
template.end = 26579700
template.add_exon((26578519, 26578725))
template.add_exon((26579325, 26579700))
template.finalize()
fai = pysam.FastaFile(
pkg_resources.resource_filename("Mikado.tests", "chr5.fas.gz"))
new5 = pad_transcript(self.reference, self.reference.deepcopy(), None,
template, fai, logger)
self.assertIn((26574970, 26575410), new5.exons)
self.assertIn((26574650, 26574820), new5.exons)
self.assertEqual(template.start, new5.start)
self.assertEqual(self.reference.end, new5.end)
new3 = pad_transcript(self.reference, self.reference.deepcopy(),
template, None, fai, logger)
self.assertIn((26578519, 26578725), new3.exons)
self.assertIn((26579325, 26579700), new3.exons)
self.assertEqual(self.reference.start, new3.start)
self.assertEqual(template.end, new5.end)
new53 = pad_transcript(self.reference, self.reference.deepcopy(),
template, template, fai, logger)
self.assertIn((26574970, 26575410), new53.exons)
self.assertIn((26574650, 26574820), new53.exons)
self.assertIn((26578519, 26578725), new53.exons)
self.assertIn((26579325, 26579700), new53.exons)
self.assertEqual(template.start, new53.start)
self.assertEqual(template.end, new53.end)
def test_locus_padding_equal_or_n(self):
for num, exons_to_add in enumerate([
((26574970, 26575410), (26578519, 26578725)),
((26574970, 26575410), (26574650, 26574820), (26578519, 26578725),
(26579325, 26579700))
]):
for num2, pad_transcripts in enumerate((False, True)):
with self.subTest(exons_to_add=exons_to_add,
pad_transcripts=pad_transcripts):
logger = create_null_logger(
"test_locus_padding_equal_or_n_" + str(num + num2 * 2))
logger.setLevel("DEBUG")
template = self.reference.copy()
del template.is_reference
template.id = "AT5G66600.3_exp"
template.unfinalize()
template.remove_exon((26575000, 26575410)) # First exon
template.remove_exon((26578519, 26578625)) # Last exon
template.start = min([_[0] for _ in exons_to_add])
template.end = max([_[1] for _ in exons_to_add])
template.add_exons(
exons_to_add) # New exon, template at 5'
template.finalize()
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
json_conf.pick.alternative_splicing.pad = pad_transcripts
locus = Locus(self.reference.copy(),
logger=logger,
configuration=json_conf)
self.assertTrue(locus[self.reference.id].is_reference)
self.assertEqual(locus.perform_padding, pad_transcripts)
locus.add_transcript_to_locus(template)
if pad_transcripts is True:
self.assertIn(template.id, locus)
locus.finalize_alternative_splicing()
self.assertNotIn(template.id, locus)
if pad_transcripts is False:
self.assertEqual(locus[self.reference.id].start,
self.reference.start)
self.assertEqual(locus[self.reference.id].end,
self.reference.end)
else:
self.assertTrue(locus.perform_padding)
self.assertEqual(locus[self.reference.id].start,
template.start,
(locus[self.reference.id].exons[0],
template.exons[0]))
self.assertEqual(
locus[self.reference.id].end, template.end,
(locus[self.reference.id].end, template.end))
self.assertNotIn(template.id, locus)
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)
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)))
@unittest.skip
def test_failed_expansion(self):
logger = create_default_logger("test_failed_expansion",
level="WARNING")
raw = [
Transcript(line, logger=logger) for line in Bed12Parser(
open(
pkg_resources.resource_filename(
"Mikado.tests",
os.path.join("test_pick_pad", "fail.bed12"))))
]
transcripts = dict((_.id, _) for _ in raw)
[_.finalize() for _ in transcripts.values()]
template = transcripts["template"] # 4535908 4540293
candidate = transcripts["candidate"] # 4536444 4540027
backup = candidate.copy()
fai = pysam.FastaFile(
pkg_resources.resource_filename(
"Mikado.tests",
os.path.join("test_pick_pad", "failing_seq.fa.gz")))
logger.setLevel("DEBUG")
candidate.logger.setLevel("DEBUG")
pad_transcript(candidate,
backup,
start_transcript=template,
end_transcript=template,
fai=fai,
logger=logger)