From 05517568aa79c886bdd7955e90934c3421a5f3fa Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 28 Jul 2016 07:41:59 +0000 Subject: [PATCH 1/3] Fix spelling in sequence name --- ariba/tests/data/reference_data_sequence_type.in.fa | 2 +- ariba/tests/data/reference_data_sequence_type.in.tsv | 2 +- ariba/tests/reference_data_test.py | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/ariba/tests/data/reference_data_sequence_type.in.fa b/ariba/tests/data/reference_data_sequence_type.in.fa index 6842c033..dd86a48a 100644 --- a/ariba/tests/data/reference_data_sequence_type.in.fa +++ b/ariba/tests/data/reference_data_sequence_type.in.fa @@ -4,5 +4,5 @@ ACGT ACGT >noncoding ACGT ->noncogind.var_only +>noncoding.var_only ACGT diff --git a/ariba/tests/data/reference_data_sequence_type.in.tsv b/ariba/tests/data/reference_data_sequence_type.in.tsv index 9f7d24ba..c02493b9 100644 --- a/ariba/tests/data/reference_data_sequence_type.in.tsv +++ b/ariba/tests/data/reference_data_sequence_type.in.tsv @@ -1,4 +1,4 @@ gene 1 0 . . . gene.var_only 1 1 . . . noncoding 0 0 . . . -noncogind.var_only 0 1 . . . +noncoding.var_only 0 1 . . . diff --git a/ariba/tests/reference_data_test.py b/ariba/tests/reference_data_test.py index 023c8816..4714e297 100644 --- a/ariba/tests/reference_data_test.py +++ b/ariba/tests/reference_data_test.py @@ -441,7 +441,7 @@ def test_sequence_type(self): ('gene', ('p', False)), ('gene.var_only', ('p', True)), ('noncoding', ('n', False)), - ('noncogind.var_only', ('n', True)), + ('noncoding.var_only', ('n', True)), ] for name, expected in tests: From c2d142a0d069a21dcd049a35db0cf03af642f0b7 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 28 Jul 2016 09:10:23 +0000 Subject: [PATCH 2/3] Bug fix reporting flag/match length of gene extended because mismatches at ends --- ariba/assembly_compare.py | 13 +- ariba/report.py | 9 +- ariba/tests/assembly_compare_test.py | 2 +- ariba/tests/cluster_test.py | 17 ++ ...er_test_full_run_ok_gene_start_mismatch.fa | 3 + ...ll_run_ok_gene_start_mismatch.metadata.tsv | 1 + ...k_gene_start_mismatch.ref_to_make_reads.fa | 7 + .../reads_1.fq | 224 ++++++++++++++++++ .../reads_2.fq | 224 ++++++++++++++++++ .../references.fa | 3 + 10 files changed, 495 insertions(+), 8 deletions(-) create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq create mode 100644 ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa diff --git a/ariba/assembly_compare.py b/ariba/assembly_compare.py index e2f7599c..ceefa1dd 100644 --- a/ariba/assembly_compare.py +++ b/ariba/assembly_compare.py @@ -33,6 +33,7 @@ def __init__(self, self.assembled_threshold = assembled_threshold self.unique_threshold = unique_threshold self.max_gene_nt_extend = max_gene_nt_extend + self.scaff_name_matching_ref = None self.gene_matching_ref = None self.gene_matching_ref_type = None self.gene_start_bases_added = None @@ -309,7 +310,7 @@ def _get_gene_matching_ref(nucmer_hits, contigs, max_end_nt_extend): if longest_match is None: return None, 'NO_MATCH', None, None else: - return AssemblyCompare._gene_from_nucmer_match(longest_match, contigs[longest_match.qry_name], max_end_nt_extend) + return (longest_match.qry_name,) + AssemblyCompare._gene_from_nucmer_match(longest_match, contigs[longest_match.qry_name], max_end_nt_extend) @staticmethod @@ -334,8 +335,8 @@ def update_flag(self, flag): if self._ref_has_region_assembled_twice(self.nucmer_hits, self.ref_sequence, self.unique_threshold): flag.add('region_assembled_twice') - ref_seq_type = self.refdata.sequence_type(self.ref_sequence.id) - if ref_seq_type != 'non_coding' and self.gene_matching_ref_type == 'GENE_FOUND': + ref_seq_type, is_variant_only = self.refdata.sequence_type(self.ref_sequence.id) + if ref_seq_type == 'p' and self.gene_matching_ref_type == 'GENE_FOUND': flag.add('complete_gene') if len(self.nucmer_hits) == 1: @@ -362,10 +363,10 @@ def run(self): self.nucmer_hits = self._parse_nucmer_coords_file(self.nucmer_coords_file, self.ref_sequence.id) self.percent_identities = self._nucmer_hits_to_percent_identity(self.nucmer_hits) self.assembled_reference_sequences = self._get_assembled_reference_sequences(self.nucmer_hits, self.ref_sequence, self.assembly_sequences) - ref_seq_type = self.refdata.sequence_type(self.ref_sequence.id) + ref_seq_type, is_variant_only = self.refdata.sequence_type(self.ref_sequence.id) if self._ref_covered_by_at_least_one_full_length_contig(self.nucmer_hits, self.assembled_threshold, self.max_gene_nt_extend): self.assembled_into_one_contig = True - if ref_seq_type != 'non_coding': - self.gene_matching_ref, self.gene_matching_ref_type, self.gene_start_bases_added, self.gene_end_bases_added = self._get_gene_matching_ref(self.nucmer_hits, self.assembly_sequences, self.max_gene_nt_extend) + if ref_seq_type == 'p': + self.scaff_name_matching_ref, self.gene_matching_ref, self.gene_matching_ref_type, self.gene_start_bases_added, self.gene_end_bases_added = self._get_gene_matching_ref(self.nucmer_hits, self.assembly_sequences, self.max_gene_nt_extend) else: self.assembled_into_one_contig = False diff --git a/ariba/report.py b/ariba/report.py index 3167a839..cc7ce3e9 100644 --- a/ariba/report.py +++ b/ariba/report.py @@ -136,6 +136,13 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum lines = [] contig_length = len(cluster.assembly.sequences[contig_name]) assert contig_length != 0 + if contig_name in ref_cov_per_contig: + if contig_name == cluster.assembly_compare.scaff_name_matching_ref: + ref_cov = len(cluster.ref_sequence) + else: + ref_cov = ref_cov_per_contig[contig_name] + else: + ref_cov = 0 common_first_columns = [ cluster.ref_sequence.id, @@ -145,7 +152,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum str(cluster.total_reads), cluster.name, str(len(cluster.ref_sequence)), - str(ref_cov_per_contig[contig_name]) if contig_name in ref_cov_per_contig else '0', # 6 ref bases assembled + str(ref_cov), str(cluster.assembly_compare.percent_identities[contig_name]) if contig_name in cluster.assembly_compare.percent_identities else '0', contig_name, str(contig_length), # 9 length of scaffold matching reference diff --git a/ariba/tests/assembly_compare_test.py b/ariba/tests/assembly_compare_test.py index 67abb68a..8d386ab4 100644 --- a/ariba/tests/assembly_compare_test.py +++ b/ariba/tests/assembly_compare_test.py @@ -324,7 +324,7 @@ def test_get_gene_matching_ref(self): } got = assembly_compare.AssemblyCompare._get_gene_matching_ref(nucmer_hits, contigs, 10) - expected = (pyfastaq.sequences.Fasta('contig.2-16', 'ATGAAATTTCCCTAG'), 'GENE_FOUND', 1, 2) + expected = ('contig', pyfastaq.sequences.Fasta('contig.2-16', 'ATGAAATTTCCCTAG'), 'GENE_FOUND', 1, 2) self.assertEqual(expected, got) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 0e5757eb..5d4b6c45 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -247,3 +247,20 @@ def test_full_run_ok_variants_only_variant_is_present(self): ] self.assertEqual(expected, c.report_lines) shutil.rmtree(tmpdir) + + + def test_full_run_ok_gene_start_mismatch(self): + '''test complete run where gene extended because too different at end for full nucmer match''' + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv') + refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) + tmpdir = 'tmp.cluster_test_full_run_ok_gene_start_mismatch' + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_gene_start_mismatch'), tmpdir) + c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=112, total_reads_bases=1080) + c.run() + expected = [ + 'gene\t1\t0\t27\t112\tcluster_name\t96\t96\t100.0\tcluster_name.scaffold.1\t364\t27.0\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\tGeneric description of gene' + ] + self.assertEqual(expected, c.report_lines) + shutil.rmtree(tmpdir) + diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa new file mode 100644 index 00000000..06e61226 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa @@ -0,0 +1,3 @@ +>gene +ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv new file mode 100644 index 00000000..b298d9ca --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv @@ -0,0 +1 @@ +gene 1 0 . . Generic description of gene diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa new file mode 100644 index 00000000..394853b6 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa @@ -0,0 +1,7 @@ +>gene +GAGCCAGATCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAA +TAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGAC +ATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCATTAAGTTCGGTGAGCAC +GACGCCCGAGGCAGTCTGAGCATTCAAAGTTGGCCTGAGCCAGATCGTAGGAGAGCGTGT +CCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAA diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq new file mode 100644 index 00000000..2abf312c --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq @@ -0,0 +1,224 @@ +@gene:1:71:181/1 +CAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:2:85:195/1 +TCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:3:43:154/1 +AAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:4:81:189/1 +AACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:5:69:180/1 +GCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:6:124:234/1 +CGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:7:76:185/1 +CTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:8:98:208/1 +CGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:9:135:247/1 +GATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:10:13:122/1 +AGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:11:82:191/1 +ACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:12:103:213/1 +ACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:13:72:182/1 +AATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:14:116:226/1 +GAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:15:70:178/1 +CCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:16:45:155/1 +AAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:17:75:185/1 +TCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:18:51:162/1 +TACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:19:53:161/1 +CAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:20:116:225/1 +GAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:21:46:155/1 +AACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:22:59:168/1 +AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:23:22:132/1 +TGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:24:38:148/1 +TTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:25:35:143/1 +AGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:26:94:205/1 +TCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:27:30:141/1 +TCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:28:125:236/1 +GTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:29:71:181.dup.2/1 +CAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:30:16:126/1 +AGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:31:73:183/1 +ATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:32:131:241/1 +AAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:33:115:226/1 +TGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:34:59:168.dup.2/1 +AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:35:84:195/1 +GTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:36:95:206/1 +CACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:37:3:113/1 +GCCAGATCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:38:33:143/1 +ACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:39:9:117/1 +TCGTAGGAGAGCGTGTCCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:40:107:217/1 +GAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:41:83:192/1 +CGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:42:135:246/1 +GATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGATGCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:43:130:238/1 +GAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:44:120:229/1 +CATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:45:59:168.dup.3/1 +AATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:46:92:202/1 +TTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:47:73:183.dup.2/1 +ATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:48:34:144/1 +CAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:49:72:182.dup.2/1 +AATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:50:86:196/1 +CGCGGATTTCACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:51:124:232/1 +CGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:52:30:138/1 +TCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCCTGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:53:25:134/1 +CCCGGTCCACAGCTTTTGAAAAACGATACAGGTGAATAAGCGCGGCCAATTCTCAGAACGTCGCGGATTTCACCGGTCACGAGAGGTTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:54:110:220/1 +GTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:55:95:205/1 +CACCGGTCACGAGAGGTTCCTGAGACATGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:56:122:231/1 +TGCGTCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq new file mode 100644 index 00000000..cbf237b3 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq @@ -0,0 +1,224 @@ +@gene:1:71:181/2 +ACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:2:85:195/2 +TCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:3:43:154/2 +GTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:4:81:189/2 +TCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:5:69:180/2 +CTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:6:124:234/2 +TTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:7:76:185/2 +GCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:8:98:208/2 +CGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:9:135:247/2 +TTCACCTGTATCGTTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:10:13:122/2 +CCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGACGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:11:82:191/2 +GCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:12:103:213/2 +GGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:13:72:182/2 +AACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:14:116:226/2 +AAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:15:70:178/2 +TTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:16:45:155/2 +CGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:17:75:185/2 +GCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:18:51:162/2 +CCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:19:53:161/2 +CTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:20:116:225/2 +AGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:21:46:155/2 +CGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:22:59:168/2 +AGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:23:22:132/2 +CATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:24:38:148/2 +CTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:25:35:143/2 +CGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:26:94:205/2 +TCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:27:30:141/2 +AACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:28:125:236/2 +CGTTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:29:71:181.dup.2/2 +ACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:30:16:126/2 +TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:31:73:183/2 +CAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:32:131:241/2 +TGTATCGTTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:33:115:226/2 +AAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:34:59:168.dup.2/2 +AGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:35:84:195/2 +TCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:36:95:206/2 +CTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:37:3:113/2 +CCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGACGCATGTCTCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:38:33:143/2 +CGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:39:9:117/2 +CTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCGCTTCGCGACGCATGTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:40:107:217/2 +ACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:41:83:192/2 +GGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:42:135:246/2 +TCACCTGTATCGTTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:43:130:238/2 +ATCGTTTTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:44:120:229/2 +CAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:45:59:168.dup.3/2 +AGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:46:92:202/2 +CCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:47:73:183.dup.2/2 +CAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:48:34:144/2 +CCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:49:72:182.dup.2/2 +AACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:50:86:196/2 +ATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCTTTCCCACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:51:124:232/2 +TTTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:52:30:138/2 +TTAATGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:53:25:134/2 +TGCATCATTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTCGCTTCATGGGTCATCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:54:110:220/2 +TGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:55:95:205/2 +TCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCGAACTTAATGCATCATTATTCCATGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@gene:56:122:231/2 +TTCAAAAGCTGTGGACCGGGACACGCTCTCCTACGATCTGGCTCAGGCCAACTTTGAATGCTCAGACTGCCTCGGGCGTCGTGCTCACCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa new file mode 100644 index 00000000..06e61226 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa @@ -0,0 +1,3 @@ +>gene +ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA From efc2b2337caed7b7a042800f8e08f01f502e0184 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 28 Jul 2016 10:00:24 +0000 Subject: [PATCH 3/3] Add -l 15 to fermilite assemblies --- ariba/tests/cluster_test.py | 8 ++++---- third_party/fermi-lite-0.1/fml-asm_ariba.cpp | 1 + 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 5d4b6c45..1d4d1854 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -184,12 +184,12 @@ def test_full_run_ok_presence_absence(self): c.run() expected = [ - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1', ] self.assertEqual(expected, c.report_lines) diff --git a/third_party/fermi-lite-0.1/fml-asm_ariba.cpp b/third_party/fermi-lite-0.1/fml-asm_ariba.cpp index e4114f65..8d529761 100644 --- a/third_party/fermi-lite-0.1/fml-asm_ariba.cpp +++ b/third_party/fermi-lite-0.1/fml-asm_ariba.cpp @@ -143,6 +143,7 @@ int assemble(char *readsFile, char *fastaOut, char* logfileOut) bseq1_t *seqs; fml_opt_init(&opt); opt.max_cnt = 10000; + opt.min_asm_ovlp = 15; std::vector minCounts; minCounts.push_back(4); minCounts.push_back(8);