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_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)
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)
def main(): parser = argparse.ArgumentParser(__doc__) parser.add_argument("-mi", "--max-intron", default=10000, dest="max_intron", type=int, help="Maximum intron length for UTR introns.") parser.add_argument("gff", type=parser_factory) parser.add_argument("out", default=sys.stdout, type=argparse.FileType("wt"), nargs="?") args = parser.parse_args() if args.max_intron < 0: raise ValueError("Max intron length <0 specified! {0}".format( args.max_intron)) ref_gff = isinstance(args.gff, GFF3) if ref_gff: form = "gff3" else: form = "gtf" current = None current_transcript = None last_header = [] for record in args.gff: if record.header is True: # print(record, file=sys.stderr) if current is not None: current = remove_introns(current, args) print(current.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='') current = None current_transcript = None print(*last_header, sep="\n", end="") last_header = [record] continue if record.feature not in ("gene", "mRNA", "CDS", "exon"): continue if record.is_gene is True and ref_gff: print(record, file=sys.stderr) last_header = [] if current is not None: # current = remove_introns(current, args) print(current.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='') current = None current_transcript = None if record.is_transcript: if ref_gff is False: if current_transcript is not None: # current_transcript = remove_introns_from_transcr(current_transcript, # args) assert current_transcript.combined_cds_length > 0 print(current_transcript, file=args.out) print(*last_header, sep="\n", file=args.out) last_header = [] elif ref_gff is True: if current_transcript is not None: if current is None: current = Gene(current_transcript) current.add(current_transcript) else: assert current_transcript.parent[0] != current.id current.add(current_transcript) # if current.id == current_transcript.parent[0]: # else: # current = remove_introns(current, args) # print(current.format(form), file=args.out) # print("###", file=args.out) # current = None # elif current_transcript is not None: # current = Gene(current_transcript) current_transcript = Transcript(record) elif record.is_exon: if record.feature not in ("CDS", "exon"): continue current_transcript.add_exon(record) else: continue continue if ref_gff and current is not None: print(*last_header, sep="\n", file=args.out) last_header = [] current = remove_introns(current, args) print(current.format(form), file=args.out) elif not ref_gff and current_transcript is not None: current_transcript = remove_introns_from_transcr( current_transcript, args) print(current_transcript.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='')
def main(): parser = argparse.ArgumentParser(__doc__) parser.add_argument("-mi", "--max-intron", default=10000, dest="max_intron", type=int, help="Maximum intron length for UTR introns.") parser.add_argument("gff", type=to_gff) parser.add_argument("out", default=sys.stdout, type=argparse.FileType("wt"), nargs="?") args = parser.parse_args() if args.max_intron < 0: raise ValueError("Max intron length <0 specified! {0}".format(args.max_intron)) ref_gff = isinstance(args.gff, GFF3) if ref_gff: form = "gff3" else: form = "gtf" current = None current_transcript = None last_header = [] for record in args.gff: if record.header is True: # print(record, file=sys.stderr) if current is not None: current = remove_introns(current, args) print(current.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='') current = None current_transcript = None print(*last_header, sep="\n", end="") last_header = [record] continue if record.feature not in ("gene", "mRNA", "CDS", "exon"): continue if record.is_gene is True and ref_gff: print(record, file=sys.stderr) last_header = [] if current is not None: # current = remove_introns(current, args) print(current.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='') current = None current_transcript = None if record.is_transcript: if ref_gff is False: if current_transcript is not None: # current_transcript = remove_introns_from_transcr(current_transcript, # args) assert current_transcript.combined_cds_length > 0 print(current_transcript, file=args.out) print(*last_header, sep="\n", file=args.out) last_header = [] elif ref_gff is True: if current_transcript is not None: if current is None: current = Gene(current_transcript) current.add(current_transcript) else: assert current_transcript.parent[0] != current.id current.add(current_transcript) # if current.id == current_transcript.parent[0]: # else: # current = remove_introns(current, args) # print(current.format(form), file=args.out) # print("###", file=args.out) # current = None # elif current_transcript is not None: # current = Gene(current_transcript) current_transcript = Transcript(record) elif record.is_exon: if record.feature not in ("CDS", "exon"): continue current_transcript.add_exon(record) else: continue continue if ref_gff and current is not None: print(*last_header, sep="\n", file=args.out) last_header = [] current = remove_introns(current, args) print(current.format(form), file=args.out) elif not ref_gff and current_transcript is not None: current_transcript = remove_introns_from_transcr(current_transcript, args) print(current_transcript.format(form), file=args.out) print(*last_header, sep="\n", file=args.out, end='')
class LocusTester(unittest.TestCase): logger = create_null_logger("locus_tester") def setUp(self): gff_transcript1 = """Chr1\tfoo\ttranscript\t101\t300\t.\t+\t.\tID=t0 Chr1\tfoo\texon\t101\t300\t.\t+\t.\tID=t0:exon1;Parent=t0 Chr1\tfoo\tCDS\t101\t250\t.\t+\t.\tID=t0:exon1;Parent=t0""".split("\n") gff_transcript1 = [GFF.GffLine(x) for x in gff_transcript1] self.assertEqual(gff_transcript1[0].chrom, "Chr1", gff_transcript1[0]) self.transcript1 = Transcript(gff_transcript1[0]) for exon in gff_transcript1[1:]: self.transcript1.add_exon(exon) self.transcript1.finalize() self.assertTrue(self.transcript1.monoexonic) self.assertEqual(self.transcript1.chrom, gff_transcript1[0].chrom) gff_transcript2 = """Chr1\tfoo\ttranscript\t101\t600\t.\t+\t.\tID=t1 Chr1\tfoo\texon\t101\t200\t.\t+\t.\tID=t1:exon1;Parent=t1 Chr1\tfoo\texon\t301\t400\t.\t+\t.\tID=t1:exon2;Parent=t1 Chr1\tfoo\texon\t501\t600\t.\t+\t.\tID=t1:exon3;Parent=t1""".split("\n") gff_transcript2 = [GFF.GffLine(x) for x in gff_transcript2] self.transcript2 = Transcript(gff_transcript2[0], logger=self.logger) for exon in gff_transcript2[1:-1]: self.transcript2.add_exon(exon) # Test that a transcript cannot be finalized if # the exons do not define the external boundaries with self.assertLogs("null", level="WARNING") as _: self.transcript2.finalize() with self.assertRaises(exceptions.ModificationError): self.transcript2.add_exon(gff_transcript2[-1]) self.transcript2.finalized = False self.transcript2.start = 101 self.transcript2.end = 600 self.transcript2.add_exon(gff_transcript2[-1]) self.transcript2.finalize() self.assertFalse(self.transcript2.monoexonic) self.assertEqual(self.transcript2.exon_num, len(gff_transcript2) - 1) # Test that trying to modify a transcript after it has been finalized causes errors with self.assertRaises(exceptions.ModificationError): for exon in gff_transcript2[1:]: self.transcript2.add_exon(exon) # Test that creating a superlocus without configuration fails with self.assertRaises(exceptions.NoJsonConfigError): _ = Superlocus(self.transcript1) self.my_json = os.path.join(os.path.dirname(__file__), "configuration.yaml") self.my_json = configurator.to_json(self.my_json) self.assertIn("scoring", self.my_json, self.my_json.keys()) 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)