[med-svn] [ariba] branch upstream updated (0600357 -> 61985a3)
Sascha Steinbiss
satta at debian.org
Thu Aug 18 15:09:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository ariba.
from 0600357 Imported Upstream version 2.1.0+ds
new 61985a3 Imported Upstream version 2.2.0+ds
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
ariba/__init__.py | 1 +
ariba/ref_genes_getter.py | 116 ++++-
ariba/ref_preparer.py | 41 +-
ariba/reference_data.py | 7 +-
ariba/report.py | 3 +-
ariba/summary.py | 289 +++++------
ariba/summary_cluster.py | 30 +-
ariba/summary_cluster_variant.py | 83 ++++
ariba/summary_sample.py | 21 +-
ariba/tasks/getref.py | 6 +-
ariba/tasks/prepareref.py | 3 +-
ariba/tasks/summary.py | 47 +-
ariba/tests/assembly_variants_test.py | 12 +-
ariba/tests/cluster_test.py | 111 +++--
ariba/tests/clusters_test.py | 24 +-
...fa => assembly_variants_one_var_one_ctg_cdg.fa} | 0
...v => assembly_variants_one_var_one_ctg_cdg.tsv} | 0
...=> assembly_variants_one_var_one_ctg_noncdg.fa} | 0
...> assembly_variants_one_var_one_ctg_noncdg.tsv} | 0
...uster_full_run_known_smtls_snp_presabs_gene.fa} | 0
..._known_smtls_snp_presabs_gene.ref_for_reads.fa} | 0
...ster_full_run_known_smtls_snp_presabs_gene.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...uster_full_run_known_smtls_snp_presabs_nonc.fa} | 0
...ster_full_run_known_smtls_snp_presabs_nonc.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
... => cluster_full_run_smtls_snp_presabs_gene.fa} | 0
...ll_run_smtls_snp_presabs_gene.ref_for_reads.fa} | 0
...=> cluster_full_run_smtls_snp_presabs_gene.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
... => cluster_full_run_smtls_snp_presabs_nonc.fa} | 0
...=> cluster_full_run_smtls_snp_presabs_nonc.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
... => cluster_full_run_smtls_snp_varonly_gene.fa} | 0
...=> cluster_full_run_smtls_snp_varonly_gene.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...> cluster_full_run_smtls_snp_varonly_gene_2.fa} | 0
... cluster_full_run_smtls_snp_varonly_gene_2.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...ster_full_run_smtls_snp_varonly_gene_no_snp.fa} | 0
...ter_full_run_smtls_snp_varonly_gene_no_snp.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
... => cluster_full_run_smtls_snp_varonly_nonc.fa} | 0
...=> cluster_full_run_smtls_snp_varonly_nonc.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...ster_full_run_smtls_snp_varonly_nonc_no_snp.fa} | 0
...ter_full_run_smtls_snp_varonly_nonc_no_snp.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...full_run_varonly.not_present.always_report.tsv} | 0
...ll_run_ok_gene_start_mismatch.ref_for_reads.fa} | 0
..._test_full_run_ok_samtools_snp_pres_abs_gene.fa | 3 -
..._full_run_ok_samtools_snp_pres_abs_noncoding.fa | 3 -
..._test_full_run_ok_samtools_snp_var_only_gene.fa | 3 -
..._full_run_ok_samtools_snp_var_only_noncoding.fa | 3 -
....fa => cluster_test_full_run_partial_asmbly.fa} | 2 +-
.../data/cluster_test_full_run_partial_asmbly.tsv | 1 +
.../reads_1.fq | 432 ++++++++++++++++
.../reads_2.fq | 432 ++++++++++++++++
.../references.fa | 2 +-
...luster_test_full_run_smtls_snp_varonly_nonc.fa} | 0
...uster_test_full_run_smtls_snp_varonly_nonc.tsv} | 0
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...cted.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
... clusters_minimap_reads_to_all_refs.clstrs.tsv} | 0
...usters_minimap_reads_to_all_refs.out.clstr2rep} | 0
...ters_minimap_reads_to_all_refs.out.clstr_count} | 0
...=> clusters_minimap_reads_to_all_refs.out.hist} | 0
...> clusters_minimap_reads_to_all_refs.out.pairs} | 0
... clusters_minimap_reads_to_all_refs.reads_1.fq} | 0
... clusters_minimap_reads_to_all_refs.reads_2.fq} | 0
...a => clusters_minimap_reads_to_all_refs.ref.fa} | 0
.../ref_preparer_test_fasta_to_metadata.coding.tsv | 3 +
.../data/ref_preparer_test_fasta_to_metadata.fa | 6 +
...f_preparer_test_fasta_to_metadata.noncoding.tsv | 3 +
.../data/ref_preparer_test_run.out/00.info.txt | 10 +-
.../ref_preparer_test_run.out/00.version_info.txt | 4 +-
.../02.cdhit.clusters.pickle | Bin 276 -> 312 bytes
.../02.cdhit.clusters.tsv | 4 +-
.../00.auto_metadata.tsv | 9 +
.../00.info.txt | 5 +
.../00.version_info.txt | 5 +
.../01.filter.check_genes.log} | 0
.../01.filter.check_metadata.log | 0
.../01.filter.check_metadata.tsv | 9 +
.../02.cdhit.all.fa | 2 +
.../02.cdhit.clusters.pickle | Bin 0 -> 344 bytes
.../02.cdhit.clusters.tsv | 6 +-
.../02.cdhit.gene.fa} | 0
.../02.cdhit.gene.varonly.fa} | 0
.../02.cdhit.noncoding.fa} | 2 +
.../02.cdhit.noncoding.varonly.fa | 0
..._cluster_w_cdhit_clstrs_file.expect.clstrs.tsv} | 0
...data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv} | 0
...ference_data_cluster_w_cdhit_clstrs_file.in.fa} | 0
...e_data_cluster_w_cdhit_clstrs_file.in.meta.tsv} | 0
...ence_data_cluster_w_cdhit_nocluster.expect.tsv} | 0
...reference_data_cluster_w_cdhit_nocluster.in.fa} | 0
...eference_data_cluster_w_cdhit_nocluster.in.tsv} | 0
ariba/tests/data/reference_data_load_fasta_file.fa | 2 +-
...ence_data_load_input_check_seq_names.bad.csv.1} | 0
...ence_data_load_input_check_seq_names.bad.csv.2} | 0
...rence_data_load_input_check_seq_names.bad.fa.1} | 0
...rence_data_load_input_check_seq_names.bad.fa.2} | 0
...nce_data_load_input_check_seq_names.good.csv.1} | 0
...nce_data_load_input_check_seq_names.good.csv.2} | 0
...ence_data_load_input_check_seq_names.good.fa.1} | 0
...ence_data_load_input_check_seq_names.good.fa.2} | 0
.../tests/data/reference_data_rename_sequences.fa | 8 +-
.../reference_data_rename_sequences_metadata.tsv | 12 +-
.../data/reference_data_test_rename_sequences.out | 10 +-
...s_variants_make_vcf_and_depths_files.asmbly.fa} | 0
...riants_make_vcf_and_depths_files.asmbly.fa.fai} | 0
...amtools_variants_make_vcf_and_depths_files.bam} | Bin
...nts_make_vcf_and_depths_files.expect.depths.gz} | Bin
...make_vcf_and_depths_files.expect.depths.gz.tbi} | Bin
..._variants_make_vcf_and_depths_files.expect.vcf} | 0
.../summary_gather_unfiltered_output_data.in.1.tsv | 6 +
.../summary_gather_unfiltered_output_data.in.2.tsv | 6 +
...ample_test_column_names_tuples_and_het_snps.tsv | 8 +-
.../summary_sample_test_column_summary_data.tsv | 8 +-
.../tests/data/summary_sample_test_var_groups.tsv | 8 +-
.../data/summary_test_gather_output_rows.in.1.tsv | 3 -
.../data/summary_test_gather_output_rows.in.2.tsv | 5 -
.../data/summary_test_get_all_cluster_names.1.tsv | 3 -
.../data/summary_test_get_all_cluster_names.2.tsv | 5 -
.../tests/data/summary_test_get_all_het_snps.1.tsv | 3 -
.../tests/data/summary_test_get_all_het_snps.2.tsv | 5 -
.../data/summary_test_get_all_var_groups.1.tsv | 3 -
.../data/summary_test_get_all_var_groups.2.tsv | 5 -
ariba/tests/data/summary_to_matrix.1.tsv | 5 +
ariba/tests/data/summary_to_matrix.2.tsv | 6 +
ariba/tests/data/vfdb_parser_test_run.out.fa | 2 +-
ariba/tests/data/vfdb_parser_test_run.out.tsv | 6 +-
ariba/tests/ref_preparer_test.py | 108 +++-
ariba/tests/reference_data_test.py | 69 ++-
ariba/tests/samtools_variants_test.py | 12 +-
ariba/tests/summary_cluster_test.py | 191 +++++---
ariba/tests/summary_cluster_variant_test.py | 67 +++
ariba/tests/summary_sample_test.py | 8 +-
ariba/tests/summary_test.py | 541 ++++++++++++---------
ariba/vfdb_parser.py | 5 +-
scripts/ariba | 26 +-
setup.py | 2 +-
167 files changed, 2133 insertions(+), 758 deletions(-)
create mode 100644 ariba/summary_cluster_variant.py
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%)
copy 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%)
copy 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%)
copy ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene => cluster_full_run_smtls_snp_varonly_gene_2}/references.fa (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_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_known_position_snp_pres_abs_gene => 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%)
copy ariba/tests/data/{cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding => 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%)
delete mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa
delete mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa
delete mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.fa
delete mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_partial_asmbly.fa} (83%)
create mode 100644 ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_partial_asmbly}/references.fa (83%)
rename ariba/tests/data/{cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.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_known_position_snp_pres_abs_noncoding => cluster_test_full_run_smtls_snp_varonly_nonc}/references.fa (100%)
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%)
create mode 100644 ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv
create mode 100644 ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa
create mode 100644 ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv
create mode 100644 ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv
create mode 100644 ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt
create mode 100644 ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt
copy ariba/tests/data/{cluster_test_init_no_reads_1/reads_2.fq => ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log} (100%)
copy ariba/tests/data/{refdata_query_prepareref => ref_preparer_test_run_all_noncoding.out}/01.filter.check_metadata.log (100%)
create mode 100644 ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv
copy ariba/tests/data/{ref_preparer_test_run.out => ref_preparer_test_run_all_noncoding.out}/02.cdhit.all.fa (90%)
create mode 100644 ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle
copy ariba/tests/data/{ref_preparer_test_run.out => ref_preparer_test_run_all_noncoding.out}/02.cdhit.clusters.tsv (53%)
copy ariba/tests/data/{cluster_test_init_no_reads_1/reads_2.fq => ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa} (100%)
copy ariba/tests/data/{cluster_test_init_no_reads_1/reads_2.fq => ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa} (100%)
copy ariba/tests/data/{ref_preparer_test_run.out/02.cdhit.all.fa => ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa} (90%)
copy ariba/tests/data/{ref_preparer_test_run.out => ref_preparer_test_run_all_noncoding.out}/02.cdhit.noncoding.varonly.fa (100%)
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%)
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%)
create mode 100644 ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv
create mode 100644 ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv
delete mode 100644 ariba/tests/data/summary_test_gather_output_rows.in.1.tsv
delete mode 100644 ariba/tests/data/summary_test_gather_output_rows.in.2.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_cluster_names.1.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_cluster_names.2.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_het_snps.1.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_het_snps.2.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_var_groups.1.tsv
delete mode 100644 ariba/tests/data/summary_test_get_all_var_groups.2.tsv
create mode 100644 ariba/tests/data/summary_to_matrix.1.tsv
create mode 100644 ariba/tests/data/summary_to_matrix.2.tsv
create mode 100644 ariba/tests/summary_cluster_variant_test.py
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