From fe8a69262399278a591c5503ae844235ee5b4739 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 4 Aug 2016 10:38:40 +0000 Subject: [PATCH 1/5] Shorten reference_data test filenames --- ...ter_w_cdhit_clstrs_file.expect.clstrs.tsv} | 0 ...cluster_w_cdhit_clstrs_file.in.clstrs.tsv} | 0 ...ce_data_cluster_w_cdhit_clstrs_file.in.fa} | 0 ...a_cluster_w_cdhit_clstrs_file.in.meta.tsv} | 0 ...data_cluster_w_cdhit_nocluster.expect.tsv} | 0 ...ence_data_cluster_w_cdhit_nocluster.in.fa} | 0 ...nce_data_cluster_w_cdhit_nocluster.in.tsv} | 0 ...data_load_input_check_seq_names.bad.csv.1} | 0 ...data_load_input_check_seq_names.bad.csv.2} | 0 ..._data_load_input_check_seq_names.bad.fa.1} | 0 ..._data_load_input_check_seq_names.bad.fa.2} | 0 ...ata_load_input_check_seq_names.good.csv.1} | 0 ...ata_load_input_check_seq_names.good.csv.2} | 0 ...data_load_input_check_seq_names.good.fa.1} | 0 ...data_load_input_check_seq_names.good.fa.2} | 0 ariba/tests/reference_data_test.py | 30 +++++++++---------- 16 files changed, 15 insertions(+), 15 deletions(-) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_clusters_in_file.expected.clusters.tsv => reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_clusters_in_file.in.clusters.tsv => reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_clusters_in_file.in.fa => reference_data_cluster_w_cdhit_clstrs_file.in.fa} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_clusters_in_file.in.meta.tsv => reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_nocluster.expected.clusters.tsv => reference_data_cluster_w_cdhit_nocluster.expect.tsv} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_nocluster.in.fa => reference_data_cluster_w_cdhit_nocluster.in.fa} (100%) rename ariba/tests/data/{reference_data_test_cluster_with_cdhit_nocluster.in.tsv => reference_data_cluster_w_cdhit_nocluster.in.tsv} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.bad.in.csv.1 => reference_data_load_input_check_seq_names.bad.csv.1} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.bad.in.csv.2 => reference_data_load_input_check_seq_names.bad.csv.2} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.bad.in.fa.1 => reference_data_load_input_check_seq_names.bad.fa.1} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.bad.in.fa.2 => reference_data_load_input_check_seq_names.bad.fa.2} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.good.in.csv.1 => reference_data_load_input_check_seq_names.good.csv.1} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.good.in.csv.2 => reference_data_load_input_check_seq_names.good.csv.2} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.good.in.fa.1 => reference_data_load_input_check_seq_names.good.fa.1} (100%) rename ariba/tests/data/{reference_data_load_input_files_and_check_seq_names.good.in.fa.2 => reference_data_load_input_check_seq_names.good.fa.2} (100%) diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.expected.clusters.tsv b/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.expected.clusters.tsv rename to ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.clusters.tsv b/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.clusters.tsv rename to ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.fa b/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.fa rename to ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.meta.tsv b/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.in.meta.tsv rename to ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.expected.clusters.tsv b/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.expected.clusters.tsv rename to ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.in.fa b/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.in.fa rename to ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa diff --git a/ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.in.tsv b/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv similarity index 100% rename from ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.in.tsv rename to ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.csv.1 b/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.csv.1 rename to ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.csv.2 b/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.csv.2 rename to ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.fa.1 b/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.fa.1 rename to ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.fa.2 b/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.bad.in.fa.2 rename to ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.csv.1 b/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.csv.1 rename to ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.csv.2 b/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.csv.2 rename to ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.fa.1 b/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.fa.1 rename to ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 diff --git a/ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.fa.2 b/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 similarity index 100% rename from ariba/tests/data/reference_data_load_input_files_and_check_seq_names.good.in.fa.2 rename to ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 diff --git a/ariba/tests/reference_data_test.py b/ariba/tests/reference_data_test.py index 4714e297..7d04d3b2 100644 --- a/ariba/tests/reference_data_test.py +++ b/ariba/tests/reference_data_test.py @@ -129,10 +129,10 @@ def test_load_all_fasta_files(self): self.assertEqual(expected, got) - def test_load_input_files_and_check_seq_names_ok(self): + def test_load_input_check_seq_names_ok(self): '''Test _load_input_files_and_check_seq_names with good input''' - fasta_files = [os.path.join(data_dir, 'reference_data_load_input_files_and_check_seq_names.good.in.fa.' + x) for x in ['1', '2']] - metadata_files = [os.path.join(data_dir, 'reference_data_load_input_files_and_check_seq_names.good.in.csv.' + x) for x in ['1', '2']] + fasta_files = [os.path.join(data_dir, 'reference_data_load_input_check_seq_names.good.fa.' + x) for x in ['1', '2']] + metadata_files = [os.path.join(data_dir, 'reference_data_load_input_check_seq_names.good.csv.' + x) for x in ['1', '2']] expected_seqs = { 'seq1': pyfastaq.sequences.Fasta('seq1', 'ACGT'), 'seq2': pyfastaq.sequences.Fasta('seq2', 'TTTT') @@ -160,10 +160,10 @@ def test_load_input_files_and_check_seq_names_ok(self): self.assertEqual(expected_meta, got_meta) - def test_load_input_files_and_check_seq_names_bad(self): + def test_load_input_check_seq_names_bad(self): '''Test _load_input_files_and_check_seq_names with bad input''' - fasta_files = [os.path.join(data_dir, 'reference_data_load_input_files_and_check_seq_names.bad.in.fa.' + x) for x in ['1', '2']] - metadata_files = [os.path.join(data_dir, 'reference_data_load_input_files_and_check_seq_names.bad.in.csv.' + x) for x in ['1', '2']] + fasta_files = [os.path.join(data_dir, 'reference_data_load_input_check_seq_names.bad.fa.' + x) for x in ['1', '2']] + metadata_files = [os.path.join(data_dir, 'reference_data_load_input_check_seq_names.bad.csv.' + x) for x in ['1', '2']] with self.assertRaises(reference_data.Error): reference_data.ReferenceData._load_input_files_and_check_seq_names(fasta_files, metadata_files) @@ -537,11 +537,11 @@ def test_cluster_with_cdhit(self): os.unlink(outprefix + '.noncoding.varonly.fa') - def test_cluster_with_cdhit_clusters_in_file(self): + def test_cluster_w_cdhit_clstrs_file(self): '''Test cluster_with_cd_hit clusters from file''' - fasta_in = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_clusters_in_file.in.fa') - meta_tsv_in = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_clusters_in_file.in.meta.tsv') - cluster_tsv_in = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_clusters_in_file.in.clusters.tsv') + fasta_in = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_clstrs_file.in.fa') + meta_tsv_in = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv') + cluster_tsv_in = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv') refdata = reference_data.ReferenceData([fasta_in], [meta_tsv_in]) outprefix = 'tmp.test_cluster_with_cdhit_clusters_in_file' @@ -555,7 +555,7 @@ def test_cluster_with_cdhit_clusters_in_file(self): got_clusters = refdata.cluster_with_cdhit(outprefix, clusters_file=cluster_tsv_in) self.assertEqual(expected_clusters, got_clusters) - expected_clusters_file = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_clusters_in_file.expected.clusters.tsv') + expected_clusters_file = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv') got_clusters_file = outprefix + '.clusters.tsv' self.assertTrue(filecmp.cmp(expected_clusters_file, got_clusters_file, shallow=False)) @@ -567,10 +567,10 @@ def test_cluster_with_cdhit_clusters_in_file(self): os.unlink(outprefix + '.noncoding.varonly.fa') - def test_cluster_with_cdhit_nocluster(self): + def test_cluster_w_cdhit_nocluster(self): '''Test cluster_with_cd_hit do not run cdhit''' - fasta_in = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_nocluster.in.fa') - tsv_in = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_nocluster.in.tsv') + fasta_in = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_nocluster.in.fa') + tsv_in = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_nocluster.in.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) outprefix = 'tmp.test_cluster_with_cdhit_nocluster' @@ -586,7 +586,7 @@ def test_cluster_with_cdhit_nocluster(self): got_clusters = refdata.cluster_with_cdhit(outprefix, nocluster=True) self.assertEqual(expected_clusters, got_clusters) - expected_clusters_file = os.path.join(data_dir, 'reference_data_test_cluster_with_cdhit_nocluster.expected.clusters.tsv') + expected_clusters_file = os.path.join(data_dir, 'reference_data_cluster_w_cdhit_nocluster.expect.tsv') got_clusters_file = outprefix + '.clusters.tsv' self.assertTrue(filecmp.cmp(expected_clusters_file, got_clusters_file, shallow=False)) From b67ce5f3f7dad672479433562c9c1810d6a23443 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 4 Aug 2016 10:44:45 +0000 Subject: [PATCH 2/5] Shorten samtools_variants test filenames --- ...ls_variants_make_vcf_and_depths_files.asmbly.fa} | 0 ...ariants_make_vcf_and_depths_files.asmbly.fa.fai} | 0 ...samtools_variants_make_vcf_and_depths_files.bam} | Bin ...ants_make_vcf_and_depths_files.expect.depths.gz} | Bin ..._make_vcf_and_depths_files.expect.depths.gz.tbi} | Bin ...s_variants_make_vcf_and_depths_files.expect.vcf} | 0 ariba/tests/samtools_variants_test.py | 12 ++++++------ 7 files changed, 6 insertions(+), 6 deletions(-) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa => samtools_variants_make_vcf_and_depths_files.asmbly.fa} (100%) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa.fai => samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai} (100%) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.bam => samtools_variants_make_vcf_and_depths_files.bam} (100%) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz => samtools_variants_make_vcf_and_depths_files.expect.depths.gz} (100%) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz.tbi => samtools_variants_make_vcf_and_depths_files.expect.depths.gz.tbi} (100%) rename ariba/tests/data/{samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf => samtools_variants_make_vcf_and_depths_files.expect.vcf} (100%) diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa.fai b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa.fai rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.bam b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.bam rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz.tbi b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz.tbi similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz.tbi rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz.tbi diff --git a/ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf b/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf similarity index 100% rename from ariba/tests/data/samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf rename to ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf diff --git a/ariba/tests/samtools_variants_test.py b/ariba/tests/samtools_variants_test.py index 873e8404..d0417bef 100644 --- a/ariba/tests/samtools_variants_test.py +++ b/ariba/tests/samtools_variants_test.py @@ -16,13 +16,13 @@ def file2lines(filename): class TestSamtoolsVariants(unittest.TestCase): - def test_make_vcf_and_read_depths_files(self): + def test_make_vcf_and_depths_files(self): '''test _make_vcf_and_read_depths_files''' - ref = os.path.join(data_dir, 'samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa') - bam = os.path.join(data_dir, 'samtools_variants_test_make_vcf_and_read_depths_files.bam') - expected_vcf = os.path.join(data_dir, 'samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf') - expected_depths = os.path.join(data_dir, 'samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz') - tmp_prefix = 'tmp.test_make_vcf_and_read_depths_files' + ref = os.path.join(data_dir, 'samtools_variants_make_vcf_and_depths_files.asmbly.fa') + bam = os.path.join(data_dir, 'samtools_variants_make_vcf_and_depths_files.bam') + expected_vcf = os.path.join(data_dir, 'samtools_variants_make_vcf_and_depths_files.expect.vcf') + expected_depths = os.path.join(data_dir, 'samtools_variants_make_vcf_and_depths_files.expect.depths.gz') + tmp_prefix = 'tmp.test_make_vcf_and_depths_files' sv = samtools_variants.SamtoolsVariants( ref, bam, From bec9a9782e0f2074d7a0f2de4188e6a136c9b28f Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 4 Aug 2016 10:50:25 +0000 Subject: [PATCH 3/5] Shorten assembly_variants test filenames --- ariba/tests/assembly_variants_test.py | 12 ++++++------ ...e.fa => assembly_variants_one_var_one_ctg_cdg.fa} | 0 ...tsv => assembly_variants_one_var_one_ctg_cdg.tsv} | 0 ...a => assembly_variants_one_var_one_ctg_noncdg.fa} | 0 ... => assembly_variants_one_var_one_ctg_noncdg.tsv} | 0 5 files changed, 6 insertions(+), 6 deletions(-) rename ariba/tests/data/{assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa => assembly_variants_one_var_one_ctg_cdg.fa} (100%) rename ariba/tests/data/{assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv => assembly_variants_one_var_one_ctg_cdg.tsv} (100%) rename ariba/tests/data/{assembly_variants_test_get_variants_non_coding.fa => assembly_variants_one_var_one_ctg_noncdg.fa} (100%) rename ariba/tests/data/{assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv => assembly_variants_one_var_one_ctg_noncdg.tsv} (100%) diff --git a/ariba/tests/assembly_variants_test.py b/ariba/tests/assembly_variants_test.py index 83d805f0..898106b3 100644 --- a/ariba/tests/assembly_variants_test.py +++ b/ariba/tests/assembly_variants_test.py @@ -102,10 +102,10 @@ def test_filter_mummer_variants(self): self.assertEqual(expected, mummer_variants) - def test_get_one_variant_for_one_contig_non_coding(self): + def test_one_var_one_ctg_noncdg(self): '''test _get_one_variant_for_one_contig_non_coding''' - fasta_in = os.path.join(data_dir, 'assembly_variants_test_get_variants_non_coding.fa') - tsv_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv') + fasta_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_noncdg.fa') + tsv_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_noncdg.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) ref_sequence_name = 'non_coding' refdata_var_dict = refdata.metadata[ref_sequence_name] @@ -144,10 +144,10 @@ def test_get_one_variant_for_one_contig_non_coding(self): self.assertEqual(expected_used_variants[i], got_used_variants) - def test_get_one_variant_for_one_contig_coding(self): + def test_one_var_one_ctg_cdg(self): '''test _get_one_variant_for_one_contig_coding''' - fasta_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa') - tsv_in = os.path.join(data_dir, 'assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv') + fasta_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_cdg.fa') + tsv_in = os.path.join(data_dir, 'assembly_variants_one_var_one_ctg_cdg.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) ref_sequence_name = 'presence_absence' ref_sequence = refdata.sequence(ref_sequence_name) diff --git a/ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa b/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa similarity index 100% rename from ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa rename to ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa diff --git a/ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv b/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv similarity index 100% rename from ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv rename to ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv diff --git a/ariba/tests/data/assembly_variants_test_get_variants_non_coding.fa b/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa similarity index 100% rename from ariba/tests/data/assembly_variants_test_get_variants_non_coding.fa rename to ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa diff --git a/ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv b/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv similarity index 100% rename from ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv rename to ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv From 3564faaff14bafbe504c3fb51c09701eddd30554 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 4 Aug 2016 10:58:00 +0000 Subject: [PATCH 4/5] Shorten clusters_test test filenames --- ariba/tests/clusters_test.py | 24 +++++++++--------- ...out.fa => clusters_cat_genes_match_ref.fa} | 0 .../00.info.txt | 0 .../01.filter.check_metadata.tsv | 0 .../02.cdhit.all.fa | 0 .../02.cdhit.clusters.pickle | Bin ...ters_minimap_reads_to_all_refs.clstrs.tsv} | 0 ...s_minimap_reads_to_all_refs.out.clstr2rep} | 0 ...minimap_reads_to_all_refs.out.clstr_count} | 0 ...usters_minimap_reads_to_all_refs.out.hist} | 0 ...sters_minimap_reads_to_all_refs.out.pairs} | 0 ...ters_minimap_reads_to_all_refs.reads_1.fq} | 0 ...ters_minimap_reads_to_all_refs.reads_2.fq} | 0 ...clusters_minimap_reads_to_all_refs.ref.fa} | 0 14 files changed, 12 insertions(+), 12 deletions(-) rename ariba/tests/data/{clusters_test_write_catted_genes_matching_refs_fasta.expected.out.fa => clusters_cat_genes_match_ref.fa} (100%) rename ariba/tests/data/{clusters_test_load_reference_data_from_dir => clusters_load_ref_data_from_dir}/00.info.txt (100%) rename ariba/tests/data/{clusters_test_load_reference_data_from_dir => clusters_load_ref_data_from_dir}/01.filter.check_metadata.tsv (100%) rename ariba/tests/data/{clusters_test_load_reference_data_from_dir => clusters_load_ref_data_from_dir}/02.cdhit.all.fa (100%) rename ariba/tests/data/{clusters_test_load_reference_data_from_dir => clusters_load_ref_data_from_dir}/02.cdhit.clusters.pickle (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.clusters.tsv => clusters_minimap_reads_to_all_refs.clstrs.tsv} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.out.cluster2representative => clusters_minimap_reads_to_all_refs.out.clstr2rep} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.out.clusterCounts => clusters_minimap_reads_to_all_refs.out.clstr_count} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.out.insertHistogram => clusters_minimap_reads_to_all_refs.out.hist} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.out.properPairs => clusters_minimap_reads_to_all_refs.out.pairs} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.reads_1.fq => clusters_minimap_reads_to_all_refs.reads_1.fq} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.reads_2.fq => clusters_minimap_reads_to_all_refs.reads_2.fq} (100%) rename ariba/tests/data/{clusters_test_minimap_reads_to_all_ref_seqs.ref.fa => clusters_minimap_reads_to_all_refs.ref.fa} (100%) diff --git a/ariba/tests/clusters_test.py b/ariba/tests/clusters_test.py index 38d1ae09..a107003e 100644 --- a/ariba/tests/clusters_test.py +++ b/ariba/tests/clusters_test.py @@ -49,9 +49,9 @@ def test_load_reference_data_info_file(self): self.assertEqual(expected, got) - def test_load_reference_data_from_dir(self): + def test_load_ref_data_from_dir(self): '''test _load_reference_data_from_dir''' - indir = os.path.join(data_dir, 'clusters_test_load_reference_data_from_dir') + indir = os.path.join(data_dir, 'clusters_load_ref_data_from_dir') got_refdata, got_clusters = clusters.Clusters._load_reference_data_from_dir(indir) expected_seq_dict = { 'variants_only1': pyfastaq.sequences.Fasta('variants_only1', 'atggcgtgcgatgaataa'), @@ -92,16 +92,16 @@ def test_load_reference_data_from_dir(self): def test_minimap_reads_to_all_ref_seqs(self): '''test test_minimap_reads_to_all_ref_seqs''' - clusters_tsv = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.clusters.tsv') - ref_fasta = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.ref.fa') - reads_1 = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.reads_1.fq') - reads_2 = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.reads_2.fq') + clusters_tsv = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.clstrs.tsv') + ref_fasta = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.ref.fa') + reads_1 = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.reads_1.fq') + reads_2 = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.reads_2.fq') tmp_outprefix = 'tmp.clusters_test_minimap_reads_to_all_ref_seqs' clusters.Clusters._minimap_reads_to_all_ref_seqs(clusters_tsv, ref_fasta, reads_1, reads_2, tmp_outprefix) - expected_cluster2rep = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.out.cluster2representative') - expected_cluster_counts = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.out.clusterCounts') - expected_proper_pairs = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.out.properPairs') - expected_insert_hist = os.path.join(data_dir, 'clusters_test_minimap_reads_to_all_ref_seqs.out.insertHistogram') + expected_cluster2rep = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.out.clstr2rep') + expected_cluster_counts = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.out.clstr_count') + expected_proper_pairs = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.out.pairs') + expected_insert_hist = os.path.join(data_dir, 'clusters_minimap_reads_to_all_refs.out.hist') # not sure that the reads order is preserved, so just check read store file exists self.assertTrue(os.path.exists(os.path.join(tmp_outprefix + '.reads'))) @@ -258,7 +258,7 @@ def __init__(self, assembled_seqs): os.unlink(tmp_file) - def test_write_catted_genes_matching_refs_fasta(self): + def test_cat_genes_match_ref(self): '''test _write_catted_genes_matching_refs_fasta''' seq1 = pyfastaq.sequences.Fasta('seq1', 'ACGT') seq3 = pyfastaq.sequences.Fasta('seq3', 'AAAA') @@ -281,7 +281,7 @@ def __init__(self, seq, seq_type, start, end): tmp_file = 'tmp.test_write_catted_genes_matching_refs_fasta.fa' self.clusters._write_catted_genes_matching_refs_fasta(tmp_file) - expected = os.path.join(data_dir, 'clusters_test_write_catted_genes_matching_refs_fasta.expected.out.fa') + expected = os.path.join(data_dir, 'clusters_cat_genes_match_ref.fa') self.assertTrue(filecmp.cmp(expected, tmp_file, shallow=False)) os.unlink(tmp_file) diff --git a/ariba/tests/data/clusters_test_write_catted_genes_matching_refs_fasta.expected.out.fa b/ariba/tests/data/clusters_cat_genes_match_ref.fa similarity index 100% rename from ariba/tests/data/clusters_test_write_catted_genes_matching_refs_fasta.expected.out.fa rename to ariba/tests/data/clusters_cat_genes_match_ref.fa diff --git a/ariba/tests/data/clusters_test_load_reference_data_from_dir/00.info.txt b/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt similarity index 100% rename from ariba/tests/data/clusters_test_load_reference_data_from_dir/00.info.txt rename to ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt diff --git a/ariba/tests/data/clusters_test_load_reference_data_from_dir/01.filter.check_metadata.tsv b/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv similarity index 100% rename from ariba/tests/data/clusters_test_load_reference_data_from_dir/01.filter.check_metadata.tsv rename to ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv diff --git a/ariba/tests/data/clusters_test_load_reference_data_from_dir/02.cdhit.all.fa b/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa similarity index 100% rename from ariba/tests/data/clusters_test_load_reference_data_from_dir/02.cdhit.all.fa rename to ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa diff --git a/ariba/tests/data/clusters_test_load_reference_data_from_dir/02.cdhit.clusters.pickle b/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle similarity index 100% rename from ariba/tests/data/clusters_test_load_reference_data_from_dir/02.cdhit.clusters.pickle rename to ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.clusters.tsv b/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.clusters.tsv rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.cluster2representative b/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.cluster2representative rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.clusterCounts b/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.clusterCounts rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.insertHistogram b/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.insertHistogram rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.properPairs b/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.out.properPairs rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.reads_1.fq b/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.reads_1.fq rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.reads_2.fq b/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.reads_2.fq rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq diff --git a/ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.ref.fa b/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa similarity index 100% rename from ariba/tests/data/clusters_test_minimap_reads_to_all_ref_seqs.ref.fa rename to ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa From 3b4221ce898247f25462f5447c196c175859c291 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 4 Aug 2016 12:48:04 +0000 Subject: [PATCH 5/5] Shorten cluster_test test filenames --- ariba/tests/cluster_test.py | 94 ++++++++++--------- ..._full_run_known_smtls_snp_presabs_gene.fa} | 0 ...n_smtls_snp_presabs_gene.ref_for_reads.fa} | 0 ...full_run_known_smtls_snp_presabs_gene.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ..._full_run_known_smtls_snp_presabs_nonc.fa} | 0 ...full_run_known_smtls_snp_presabs_nonc.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ...luster_full_run_smtls_snp_presabs_gene.fa} | 0 ...n_smtls_snp_presabs_gene.ref_for_reads.fa} | 0 ...uster_full_run_smtls_snp_presabs_gene.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ...luster_full_run_smtls_snp_presabs_nonc.fa} | 0 ...uster_full_run_smtls_snp_presabs_nonc.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ...luster_full_run_smtls_snp_varonly_gene.fa} | 0 ...uster_full_run_smtls_snp_varonly_gene.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ...ster_full_run_smtls_snp_varonly_gene_2.fa} | 0 ...ter_full_run_smtls_snp_varonly_gene_2.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa} | 0 ...full_run_smtls_snp_varonly_gene_no_snp.fa} | 0 ...ull_run_smtls_snp_varonly_gene_no_snp.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa} | 0 ...luster_full_run_smtls_snp_varonly_nonc.fa} | 0 ...uster_full_run_smtls_snp_varonly_nonc.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa | 0 ...full_run_smtls_snp_varonly_nonc_no_snp.fa} | 0 ...ull_run_smtls_snp_varonly_nonc_no_snp.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa} | 0 ...run_varonly.not_present.always_report.tsv} | 0 ...n_ok_gene_start_mismatch.ref_for_reads.fa} | 0 ...r_test_full_run_smtls_snp_varonly_nonc.fa} | 0 ..._test_full_run_smtls_snp_varonly_nonc.tsv} | 0 .../reads_1.fq | 0 .../reads_2.fq | 0 .../references.fa} | 0 55 files changed, 48 insertions(+), 46 deletions(-) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa => cluster_full_run_known_smtls_snp_presabs_gene.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa => cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv => cluster_full_run_known_smtls_snp_presabs_gene.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene => cluster_full_run_known_smtls_snp_presabs_gene}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene => cluster_full_run_known_smtls_snp_presabs_gene}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var => cluster_full_run_known_smtls_snp_presabs_gene}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa => cluster_full_run_known_smtls_snp_presabs_nonc.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv => cluster_full_run_known_smtls_snp_presabs_nonc.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding => cluster_full_run_known_smtls_snp_presabs_nonc}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding => cluster_full_run_known_smtls_snp_presabs_nonc}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var => cluster_full_run_known_smtls_snp_presabs_nonc}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa => cluster_full_run_smtls_snp_presabs_gene.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa => cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv => cluster_full_run_smtls_snp_presabs_gene.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var => cluster_full_run_smtls_snp_presabs_gene}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var => cluster_full_run_smtls_snp_presabs_gene}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene => cluster_full_run_smtls_snp_presabs_gene}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa => cluster_full_run_smtls_snp_presabs_nonc.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv => cluster_full_run_smtls_snp_presabs_nonc.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var => cluster_full_run_smtls_snp_presabs_nonc}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var => cluster_full_run_smtls_snp_presabs_nonc}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding => cluster_full_run_smtls_snp_presabs_nonc}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa => cluster_full_run_smtls_snp_varonly_gene.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv => cluster_full_run_smtls_snp_varonly_gene.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var => cluster_full_run_smtls_snp_varonly_gene}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var => cluster_full_run_smtls_snp_varonly_gene}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_gene => cluster_full_run_smtls_snp_varonly_gene}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa => cluster_full_run_smtls_snp_varonly_gene_2.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv => cluster_full_run_smtls_snp_varonly_gene_2.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var => cluster_full_run_smtls_snp_varonly_gene_2}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var => cluster_full_run_smtls_snp_varonly_gene_2}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa => cluster_full_run_smtls_snp_varonly_gene_2/references.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa => cluster_full_run_smtls_snp_varonly_gene_no_snp.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv => cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene => cluster_full_run_smtls_snp_varonly_gene_no_snp}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_gene => cluster_full_run_smtls_snp_varonly_gene_no_snp}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_gene.fa => cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa => cluster_full_run_smtls_snp_varonly_nonc.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv => cluster_full_run_smtls_snp_varonly_nonc.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding => cluster_full_run_smtls_snp_varonly_nonc}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding => cluster_full_run_smtls_snp_varonly_nonc}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_noncoding => cluster_full_run_smtls_snp_varonly_nonc}/references.fa (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa => cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv => cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_gene => cluster_full_run_smtls_snp_varonly_nonc_no_snp}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_gene => cluster_full_run_smtls_snp_varonly_nonc_no_snp}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa => cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_variants_only.not_present.always_report.metadata.tsv => cluster_full_run_varonly.not_present.always_report.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.ref_to_make_reads.fa => cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa => cluster_test_full_run_smtls_snp_varonly_nonc.fa} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv => cluster_test_full_run_smtls_snp_varonly_nonc.tsv} (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_noncoding => cluster_test_full_run_smtls_snp_varonly_nonc}/reads_1.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_noncoding => cluster_test_full_run_smtls_snp_varonly_nonc}/reads_2.fq (100%) rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa => cluster_test_full_run_smtls_snp_varonly_nonc/references.fa} (100%) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 7b7de6a5..e2cacf8a 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -216,9 +216,9 @@ def test_full_run_ok_variants_only_variant_not_present(self): def test_full_run_ok_variants_only_variant_not_present_always_report(self): '''test complete run of cluster on a variants only gene when variant not present but always report variant''' fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only.not_present.always_report.metadata.tsv') + tsv_in = os.path.join(data_dir, 'cluster_full_run_varonly.not_present.always_report.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) - tmpdir = 'tmp.cluster_test_full_run_ok_variants_only.not_present.always_report' + tmpdir = 'tmp.cluster_full_run_varonly.not_present.always_report' shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=66, total_reads_bases=3300) @@ -265,13 +265,13 @@ def test_full_run_ok_gene_start_mismatch(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_pres_abs_gene(self): + def test_full_run_smtls_snp_presabs_gene(self): '''test complete run where samtools calls a snp in a presence/absence gene''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_gene' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_gene'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_gene'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() expected = [ @@ -281,13 +281,15 @@ def test_full_run_ok_samtools_snp_pres_abs_gene(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_var_only_gene(self): + def test_full_run_smtls_snp_varonly_gene_2(self): '''test complete run where samtools calls a snp in a variant only gene''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv') + # _2 because I think test_full_run_smtls_snp_varonly_gene tests the asame functionality. + # ... but let's leave both tests in anyway + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) - tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_gene' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_gene'), tmpdir) + tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_gene_2' + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_2'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() expected = [ @@ -297,13 +299,13 @@ def test_full_run_ok_samtools_snp_var_only_gene(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_pres_abs_gene(self): + def test_full_run_known_smtls_snp_presabs_gene(self): '''test complete run where samtools calls a snp at a known snp location in a presence/absence gene''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_gene'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() @@ -316,13 +318,13 @@ def test_full_run_ok_samtools_snp_known_position_pres_abs_gene(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var(self): + def test_full_run_smtls_snp_varonly_gene_no_snp(self): '''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) - tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var'), tmpdir) + tmpdir = 'tmp.cluster_test_full_run_smtls_snp_varonly_gene_no_snp' + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene_no_snp'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() @@ -335,13 +337,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var(self): + def test_full_run_smtls_snp_varonly_gene(self): '''test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_gene'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() @@ -354,13 +356,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var(sel shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_pres_abs_noncoding(self): + def test_full_run_smtls_snp_presabs_nonc(self): '''test complete run where samtools calls a snp in a presence/absence noncoding sequence''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) - tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding'), tmpdir) + tmpdir = 'tmp.cluster_test_full_run_smtls_snp_presabs_nonc' + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_presabs_nonc'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() expected = [ @@ -370,13 +372,13 @@ def test_full_run_ok_samtools_snp_pres_abs_noncoding(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_var_only_noncoding(self): + def test_full_run_smtls_snp_varonly_nonc(self): '''test complete run where samtools calls a snp in a presence/absence noncoding sequence''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) - tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_var_only_noncoding' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_var_only_noncoding'), tmpdir) + tmpdir = 'tmp.cluster_full_run_smtls_snp_varonly_nonc' + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() expected = [ @@ -386,13 +388,13 @@ def test_full_run_ok_samtools_snp_var_only_noncoding(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding(self): + def test_full_run_known_smtls_snp_presabs_nonc(self): '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_known_smtls_snp_presabs_nonc'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() @@ -405,13 +407,13 @@ def test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding(self): shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var(self): + def test_full_run_smtls_snp_varonly_nonc_no_snp(self): '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa') + tsv_in = os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_full_run_smtls_snp_varonly_nonc_no_snp'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() @@ -424,13 +426,13 @@ def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_hav shutil.rmtree(tmpdir) - def test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var(self): + def test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc(self): '''test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var''' - fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa') - tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv') + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc.tsv') refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) tmpdir = 'tmp.cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding' - shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var'), tmpdir) + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_smtls_snp_varonly_nonc'), tmpdir) c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=148, total_reads_bases=13320) c.run() diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/references.fa rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/references.fa b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/references.fa rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/references.fa rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/references.fa b/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/references.fa rename to ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/references.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/references.fa b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/references.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/references.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/references.fa b/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/references.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/references.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/references.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq b/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq similarity index 100% rename from ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq rename to ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq diff --git a/ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/references.fa 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