[med-svn] [ariba] 02/03: Merge tag 'upstream/2.2.0+ds'
Sascha Steinbiss
satta at debian.org
Thu Aug 18 15:09:53 UTC 2016
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satta pushed a commit to branch master
in repository ariba.
commit b8f92a1279024c2f6a3b113cc3855e3a380957bf
Merge: 452fbf3 61985a3
Author: Sascha Steinbiss <satta at debian.org>
Date: Thu Aug 18 15:02:12 2016 +0000
Merge tag 'upstream/2.2.0+ds'
Upstream version 2.2.0+ds
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 | 18 +
.../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 | 18 +
.../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, 2165 insertions(+), 758 deletions(-)
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