def test_monoexonic(self):
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
fasta = self.fasta[model.chrom][model.start - 1: model.end]
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
neg = model.copy()
neg.strand = "-"
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
def test_monoexonic(self):
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
fasta = self.fasta[model.chrom][model.start - 1:model.end]
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
neg = model.copy()
neg.strand = "-"
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
def __prepare_transcript(self, prediction: Transcript):
"""
Private method that checks that a prediction transcript is OK
before starting to analyse its concordance with the reference.
:param prediction:
:return:
"""
# Prepare the prediction to be analysed
prediction.logger = self.logger
try:
prediction.finalize()
# noinspection PyUnresolvedReferences
if self.args.exclude_utr is True:
prediction.remove_utrs()
except InvalidCDS:
try:
prediction.strip_cds()
except InvalidTranscript as err:
self.logger.warn("Invalid transcript (due to CDS): %s",
prediction.id)
self.logger.warn("Error message: %s", err)
self.done += 1
self.print_tmap(None)
return None
except InvalidTranscript as err:
# args.queue.put_nowait("mock")
self.logger.warn("Invalid transcript: %s", prediction.id)
self.logger.warn("Error message: %s", err)
self.done += 1
self.print_tmap(None)
return None
return prediction
def __prepare_transcript(self, prediction: Transcript):
"""
Private method that checks that a prediction transcript is OK
before starting to analyse its concordance with the reference.
:param prediction:
:return:
"""
# Prepare the prediction to be analysed
prediction.logger = self.logger
try:
prediction.finalize()
# noinspection PyUnresolvedReferences
if self.args.exclude_utr is True:
prediction.remove_utrs()
except InvalidCDS:
try:
prediction.strip_cds()
except InvalidTranscript as err:
self.logger.warn("Invalid transcript (due to CDS): %s",
prediction.id)
self.logger.warn("Error message: %s", err)
self.done += 1
self.print_tmap(None)
return None
except InvalidTranscript as err:
# args.queue.put_nowait("mock")
self.logger.warn("Invalid transcript: %s", prediction.id)
self.logger.warn("Error message: %s", err)
self.done += 1
self.print_tmap(None)
return None
return prediction
def test_positive_strand(self):
gtf_lines = """chr1A Self_CESAR/windows_chr1A.gp transcript 265021906 265026255 . + . gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1";
chr1A Self_CESAR/windows_chr1A.gp exon 265021906 265021971 . + . gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "1"; exon_id "TraesCS1A01G152900.1.1";
chr1A Self_CESAR/windows_chr1A.gp CDS 265021906 265021971 . + 0 gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "1"; exon_id "TraesCS1A01G152900.1.1";
chr1A Self_CESAR/windows_chr1A.gp exon 265022056 265026255 . + . gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "2"; exon_id "TraesCS1A01G152900.1.2";
chr1A Self_CESAR/windows_chr1A.gp CDS 265022056 265026252 . + 0 gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "2"; exon_id "TraesCS1A01G152900.1.2";
chr1A Self_CESAR/windows_chr1A.gp start_codon 265021906 265021908 . + 0 gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "1"; exon_id "TraesCS1A01G152900.1.1";
chr1A Self_CESAR/windows_chr1A.gp stop_codon 265026253 265026255 . + 0 gene_id "TraesCS1A01G152900.1"; transcript_id "TraesCS1A01G152900.1"; exon_number "2"; exon_id "TraesCS1A01G152900.1.2";"""
gtf_lines = [GtfLine(_) for _ in gtf_lines.split("\n")]
t = Transcript(gtf_lines[0])
t.add_exons(gtf_lines[1:])
t.finalize()
self.assertEqual(t.start, t.combined_cds_start)
self.assertEqual(t.end, t.combined_cds_end)
def test_negative(self):
gtf_lines = """Chr5 Cufflinks transcript 26575364 26578163 1000 - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";exon_number "1";FPKM "2.9700103727";conf_hi "3.260618";frac "0.732092";cov "81.895309";conf_lo "2.679403";
Chr5 Cufflinks exon 26575364 26575410 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575495 26575620 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575711 26575797 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575885 26575944 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576035 26576134 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576261 26577069 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577163 26577288 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577378 26577449 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577856 26578163 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";"""
gtf_lines = [GtfLine(line) for line in gtf_lines.split("\n")]
self.assertEqual(len([_ for _ in gtf_lines if _.header]), 0)
transcript = Transcript(gtf_lines[0])
transcript.add_exons(gtf_lines[1:])
transcript.finalize()
fasta_seq = self.fasta[transcript.chrom][transcript.start -
1:transcript.end]
tr_neg = transcript.copy()
tchecker = TranscriptChecker(tr_neg, fasta_seq, strand_specific=False)
self.assertEqual(tchecker.strand, "-")
self.assertEqual(tchecker.fasta_seq, fasta_seq)
tchecker.check_strand()
self.assertEqual(tchecker.strand, "-")
tr_neg = transcript.copy()
tr_neg.strand = "+"
for ss in (False, True):
with self.subTest(ss=ss):
tchecker = TranscriptChecker(tr_neg.copy(),
fasta_seq,
strand_specific=ss)
tchecker.check_strand()
if ss:
self.assertEqual(tchecker.strand, "+")
self.assertTrue(tchecker.suspicious_splicing)
else:
self.assertEqual(tchecker.strand, "-")
def test_monoexonic_suspicious(self):
"""A monoexonic transcript should never appear as a suspicious transcript, in terms of splicing."""
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
del model.attributes["canonical_number"]
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(model.suspicious_splicing)
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
del model.attributes["canonical_on_reverse_strand"]
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
del model.attributes["canonical_on_reverse_strand"]
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
def test_negative(self):
gtf_lines = """Chr5 Cufflinks transcript 26575364 26578163 1000 - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";exon_number "1";FPKM "2.9700103727";conf_hi "3.260618";frac "0.732092";cov "81.895309";conf_lo "2.679403";
Chr5 Cufflinks exon 26575364 26575410 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575495 26575620 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575711 26575797 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575885 26575944 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576035 26576134 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576261 26577069 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577163 26577288 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577378 26577449 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577856 26578163 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";"""
gtf_lines = [GtfLine(line) for line in gtf_lines.split("\n")]
self.assertEqual(len([_ for _ in gtf_lines if _.header]), 0)
transcript = Transcript(gtf_lines[0])
transcript.add_exons(gtf_lines[1:])
transcript.finalize()
fasta_seq = self.fasta[transcript.chrom][transcript.start - 1:transcript.end]
tr_neg = transcript.copy()
tchecker = TranscriptChecker(tr_neg, fasta_seq, strand_specific=False)
self.assertEqual(tchecker.strand, "-")
self.assertEqual(tchecker.fasta_seq, fasta_seq)
tchecker.check_strand()
self.assertEqual(tchecker.strand, "-")
tr_neg = transcript.copy()
tr_neg.strand = "+"
for ss in (False, True):
with self.subTest(ss=ss):
tchecker = TranscriptChecker(tr_neg.copy(), fasta_seq, strand_specific=ss)
tchecker.check_strand()
if ss:
self.assertEqual(tchecker.strand, "+")
self.assertTrue(tchecker.suspicious_splicing)
else:
self.assertEqual(tchecker.strand, "-")
def test_monoexonic_suspicious(self):
"""A monoexonic transcript should never appear as a suspicious transcript, in terms of splicing."""
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
del model.attributes["canonical_number"]
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(model.suspicious_splicing)
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
del model.attributes["canonical_on_reverse_strand"]
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
del model.attributes["canonical_on_reverse_strand"]
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
class TChekerTester(unittest.TestCase):
temp_genome = None
@classmethod
def setUpClass(cls):
# Prepare the genome
cls.temp_genome = tempfile.NamedTemporaryFile(mode="wb", suffix=".fa")
with pkg_resources.resource_stream("Mikado.tests",
"chr5.fas.gz") as comp:
cls.temp_genome.write(gzip.decompress(comp.read()))
cls.temp_genome.flush()
cls.fasta = pyfaidx.Fasta(cls.temp_genome.name)
def setUp(self):
# Prepare the model
self.model_lines = """Chr5 tair10 transcript 26584797 26595528 100 + . ID=c58_g1_i3.mrna1.19;Parent=c58_g1_i3.path1.19;Name=c58_g1_i3.mrna1.19;gene_name=c58_g1_i3
Chr5 tair10 exon 26584797 26584879 . + . ID=c58_g1_i3.mrna1.19.exon1;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585220 26585273 . + . ID=c58_g1_i3.mrna1.19.exon2;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585345 26585889 . + . ID=c58_g1_i3.mrna1.19.exon3;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585982 26586294 . + . ID=c58_g1_i3.mrna1.19.exon4;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586420 26586524 . + . ID=c58_g1_i3.mrna1.19.exon5;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586638 26586850 . + . ID=c58_g1_i3.mrna1.19.exon6;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586934 26586996 . + . ID=c58_g1_i3.mrna1.19.exon7;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587084 26587202 . + . ID=c58_g1_i3.mrna1.19.exon8;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587287 26587345 . + . ID=c58_g1_i3.mrna1.19.exon9;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587427 26587472 . + . ID=c58_g1_i3.mrna1.19.exon10;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26595411 26595528 . + . ID=c58_g1_i3.mrna1.19.exon11;Parent=c58_g1_i3.mrna1.19"""
self.gff_lines = []
for line in self.model_lines.split("\n"):
line = line.rstrip().lstrip()
line = GffLine(line)
self.gff_lines.append(line)
self.model = Transcript(self.gff_lines[0])
self.model.add_exons(self.gff_lines[1:])
self.model.finalize()
self.exons = [
self.fasta[line.chrom][line.start - 1:line.end]
for line in self.gff_lines[1:]
]
self.assertEqual(sum([len(exon) for exon in self.exons]), 1718,
self.exons)
# We need the whole genomic fragment
self.model_fasta = self.fasta["Chr5"][self.model.start -
1:self.model.end]
self.assertEqual(self.gff_lines[1].start, 26584797)
self.assertEqual(self.gff_lines[1].end, 26584879)
self.assertEqual(self.model.exons[0][0], self.gff_lines[1].start)
self.assertEqual(self.model.exons[0][1], self.gff_lines[1].end)
@classmethod
def tearDownClass(cls):
# Remove the genome
if hasattr(cls.temp_genome, "close"):
cls.temp_genome.close()
cls.fasta.close()
os.remove("{}.fai".format(cls.temp_genome.name))
def test_translation_table(self):
self.assertEqual(TranscriptChecker.get_translation_table(), {
65: 84,
67: 71,
71: 67,
84: 65
})
def test_rev_complement(self):
string = "AGTCGTGCAGNGTCGAAGTGCAACAGTGC"
self.assertEqual(TranscriptChecker.rev_complement(string),
"GCACTGTTGCACTTCGACNCTGCACGACT")
def test_init(self):
tcheck = TranscriptChecker(self.model, self.model_fasta)
self.assertEqual(tcheck.cdna_length, 1718)
self.assertEqual(
sorted(tcheck.exons),
sorted([(exon.start, exon.end) for exon in self.exons]))
self.assertEqual(tcheck.fasta_seq, self.model_fasta)
def test_check_reverse_strand(self):
self.model.strand = "-"
tcheck = TranscriptChecker(self.model,
self.model_fasta,
strand_specific=False)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
def test_check_strand_not_reversed(self):
self.model.strand = "-"
tcheck = TranscriptChecker(self.model,
self.model_fasta,
strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
self.assertTrue(tcheck.attributes["canonical_on_reverse_strand"])
self.assertTrue(tcheck.suspicious_splicing)
def test_monoexonic(self):
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
fasta = self.fasta[model.chrom][model.start - 1:model.end]
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
neg = model.copy()
neg.strand = "-"
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
def test_negative(self):
gtf_lines = """Chr5 Cufflinks transcript 26575364 26578163 1000 - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";exon_number "1";FPKM "2.9700103727";conf_hi "3.260618";frac "0.732092";cov "81.895309";conf_lo "2.679403";
Chr5 Cufflinks exon 26575364 26575410 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575495 26575620 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575711 26575797 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575885 26575944 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576035 26576134 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576261 26577069 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577163 26577288 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577378 26577449 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577856 26578163 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";"""
gtf_lines = [GtfLine(line) for line in gtf_lines.split("\n")]
self.assertEqual(len([_ for _ in gtf_lines if _.header]), 0)
transcript = Transcript(gtf_lines[0])
transcript.add_exons(gtf_lines[1:])
transcript.finalize()
fasta_seq = self.fasta[transcript.chrom][transcript.start -
1:transcript.end]
tr_neg = transcript.copy()
tchecker = TranscriptChecker(tr_neg, fasta_seq, strand_specific=False)
self.assertEqual(tchecker.strand, "-")
self.assertEqual(tchecker.fasta_seq, fasta_seq)
tchecker.check_strand()
self.assertEqual(tchecker.strand, "-")
tr_neg = transcript.copy()
tr_neg.strand = "+"
for ss in (False, True):
with self.subTest(ss=ss):
tchecker = TranscriptChecker(tr_neg.copy(),
fasta_seq,
strand_specific=ss)
tchecker.check_strand()
if ss:
self.assertEqual(tchecker.strand, "+")
self.assertTrue(tchecker.suspicious_splicing)
else:
self.assertEqual(tchecker.strand, "-")
def test_suspicious(self):
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
del self.model.attributes["mixed_splices"]
self.assertFalse(self.model.suspicious_splicing)
self.model.attributes["canonical_number"] = 0
self.assertFalse(self.model.suspicious_splicing)
del self.model.attributes["canonical_number"]
self.model.attributes["canonical_on_reverse_strand"] = True
self.assertTrue(self.model.suspicious_splicing)
self.model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(self.model.suspicious_splicing)
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
del self.model.attributes["mixed_splices"]
del self.model.attributes["canonical_on_reverse_strand"]
self.model.attributes["canonical_number"] = 0
self.assertFalse(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
self.model.attributes["canonical_on_reverse_strand"] = True
self.assertTrue(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
del self.model.attributes["canonical_on_reverse_strand"]
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
def test_monoexonic_suspicious(self):
"""A monoexonic transcript should never appear as a suspicious transcript, in terms of splicing."""
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
del model.attributes["canonical_number"]
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(model.suspicious_splicing)
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
del model.attributes["canonical_on_reverse_strand"]
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
del model.attributes["canonical_on_reverse_strand"]
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
class TChekerTester(unittest.TestCase):
temp_genome = None
@classmethod
def setUpClass(cls):
# Prepare the genome
cls.temp_genome = tempfile.NamedTemporaryFile(mode="wb", suffix=".fa")
with pkg_resources.resource_stream("Mikado.tests", "chr5.fas.gz") as comp:
cls.temp_genome.write(gzip.decompress(comp.read()))
cls.temp_genome.flush()
cls.fasta = pyfaidx.Fasta(cls.temp_genome.name)
def setUp(self):
# Prepare the model
self.model_lines= """Chr5 tair10 transcript 26584797 26595528 100 + . ID=c58_g1_i3.mrna1.19;Parent=c58_g1_i3.path1.19;Name=c58_g1_i3.mrna1.19;gene_name=c58_g1_i3
Chr5 tair10 exon 26584797 26584879 . + . ID=c58_g1_i3.mrna1.19.exon1;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585220 26585273 . + . ID=c58_g1_i3.mrna1.19.exon2;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585345 26585889 . + . ID=c58_g1_i3.mrna1.19.exon3;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26585982 26586294 . + . ID=c58_g1_i3.mrna1.19.exon4;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586420 26586524 . + . ID=c58_g1_i3.mrna1.19.exon5;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586638 26586850 . + . ID=c58_g1_i3.mrna1.19.exon6;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26586934 26586996 . + . ID=c58_g1_i3.mrna1.19.exon7;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587084 26587202 . + . ID=c58_g1_i3.mrna1.19.exon8;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587287 26587345 . + . ID=c58_g1_i3.mrna1.19.exon9;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26587427 26587472 . + . ID=c58_g1_i3.mrna1.19.exon10;Parent=c58_g1_i3.mrna1.19
Chr5 tair10 exon 26595411 26595528 . + . ID=c58_g1_i3.mrna1.19.exon11;Parent=c58_g1_i3.mrna1.19"""
self.gff_lines = []
for line in self.model_lines.split("\n"):
line = line.rstrip().lstrip()
line = GffLine(line)
self.gff_lines.append(line)
self.model = Transcript(self.gff_lines[0])
self.model.add_exons(self.gff_lines[1:])
self.model.finalize()
self.exons = [self.fasta[line.chrom][line.start - 1:line.end] for line in self.gff_lines[1:]]
self.assertEqual(sum([len(exon) for exon in self.exons]), 1718, self.exons)
# We need the whole genomic fragment
self.model_fasta = self.fasta["Chr5"][self.model.start -1:self.model.end]
self.assertEqual(self.gff_lines[1].start, 26584797)
self.assertEqual(self.gff_lines[1].end, 26584879)
self.assertEqual(self.model.exons[0][0], self.gff_lines[1].start)
self.assertEqual(self.model.exons[0][1], self.gff_lines[1].end)
@classmethod
def tearDownClass(cls):
# Remove the genome
if hasattr(cls.temp_genome, "close"):
cls.temp_genome.close()
cls.fasta.close()
os.remove("{}.fai".format(cls.temp_genome.name))
def test_translation_table(self):
self.assertEqual(TranscriptChecker.get_translation_table(),
{65: 84, 67: 71, 71: 67, 84: 65})
def test_rev_complement(self):
string = "AGTCGTGCAGNGTCGAAGTGCAACAGTGC"
self.assertEqual(TranscriptChecker.rev_complement(string),
"GCACTGTTGCACTTCGACNCTGCACGACT")
def test_init(self):
tcheck = TranscriptChecker(self.model, self.model_fasta)
self.assertEqual(tcheck.cdna_length, 1718)
self.assertEqual(sorted(tcheck.exons), sorted([(exon.start, exon.end) for exon in self.exons]))
self.assertEqual(tcheck.fasta_seq, self.model_fasta)
def test_check_reverse_strand(self):
self.model.strand = "-"
tcheck = TranscriptChecker(self.model, self.model_fasta, strand_specific=False)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
def test_check_strand_not_reversed(self):
self.model.strand = "-"
tcheck = TranscriptChecker(self.model, self.model_fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
self.assertTrue(tcheck.attributes["canonical_on_reverse_strand"])
self.assertTrue(tcheck.suspicious_splicing)
def test_monoexonic(self):
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
fasta = self.fasta[model.chrom][model.start - 1: model.end]
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(model.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "+")
neg = model.copy()
neg.strand = "-"
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=False)
tcheck.check_strand()
self.assertIsNone(tcheck.strand)
tcheck = TranscriptChecker(neg.copy(), fasta, strand_specific=True)
tcheck.check_strand()
self.assertEqual(tcheck.strand, "-")
def test_negative(self):
gtf_lines = """Chr5 Cufflinks transcript 26575364 26578163 1000 - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";exon_number "1";FPKM "2.9700103727";conf_hi "3.260618";frac "0.732092";cov "81.895309";conf_lo "2.679403";
Chr5 Cufflinks exon 26575364 26575410 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575495 26575620 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575711 26575797 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26575885 26575944 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576035 26576134 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26576261 26577069 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577163 26577288 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577378 26577449 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";
Chr5 Cufflinks exon 26577856 26578163 . - . gene_id "cufflinks_star_at.23553";transcript_id "cufflinks_star_at.23553.1";"""
gtf_lines = [GtfLine(line) for line in gtf_lines.split("\n")]
self.assertEqual(len([_ for _ in gtf_lines if _.header]), 0)
transcript = Transcript(gtf_lines[0])
transcript.add_exons(gtf_lines[1:])
transcript.finalize()
fasta_seq = self.fasta[transcript.chrom][transcript.start - 1:transcript.end]
tr_neg = transcript.copy()
tchecker = TranscriptChecker(tr_neg, fasta_seq, strand_specific=False)
self.assertEqual(tchecker.strand, "-")
self.assertEqual(tchecker.fasta_seq, fasta_seq)
tchecker.check_strand()
self.assertEqual(tchecker.strand, "-")
tr_neg = transcript.copy()
tr_neg.strand = "+"
for ss in (False, True):
with self.subTest(ss=ss):
tchecker = TranscriptChecker(tr_neg.copy(), fasta_seq, strand_specific=ss)
tchecker.check_strand()
if ss:
self.assertEqual(tchecker.strand, "+")
self.assertTrue(tchecker.suspicious_splicing)
else:
self.assertEqual(tchecker.strand, "-")
def test_suspicious(self):
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
del self.model.attributes["mixed_splices"]
self.assertFalse(self.model.suspicious_splicing)
self.model.attributes["canonical_number"] = 0
self.assertFalse(self.model.suspicious_splicing)
del self.model.attributes["canonical_number"]
self.model.attributes["canonical_on_reverse_strand"] = True
self.assertTrue(self.model.suspicious_splicing)
self.model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(self.model.suspicious_splicing)
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
del self.model.attributes["mixed_splices"]
del self.model.attributes["canonical_on_reverse_strand"]
self.model.attributes["canonical_number"] = 0
self.assertFalse(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
self.model.attributes["canonical_on_reverse_strand"] = True
self.assertTrue(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
del self.model.attributes["canonical_on_reverse_strand"]
self.model.attributes["mixed_splices"] = "6positive,1negative"
self.assertTrue(self.model.suspicious_splicing)
self.assertTrue(self.model.only_non_canonical_splicing)
def test_monoexonic_suspicious(self):
"""A monoexonic transcript should never appear as a suspicious transcript, in terms of splicing."""
exon = self.gff_lines[1]
transcript_line = self.gff_lines[0]
transcript_line.end = exon.end
model = Transcript(transcript_line)
model.add_exon(exon)
model.finalize()
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
del model.attributes["canonical_number"]
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
model.attributes["canonical_on_reverse_strand"] = False
self.assertFalse(model.suspicious_splicing)
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
del model.attributes["mixed_splices"]
del model.attributes["canonical_on_reverse_strand"]
model.attributes["canonical_number"] = 0
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
model.attributes["canonical_on_reverse_strand"] = True
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)
del model.attributes["canonical_on_reverse_strand"]
model.attributes["mixed_splices"] = "6positive,1negative"
self.assertFalse(model.suspicious_splicing)
self.assertFalse(model.only_non_canonical_splicing)