2.2.0+ds'

Sascha Steinbiss Thu, 18 Aug 2016 08:10:18 -0700

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satta pushed a commit to branch master
in repository ariba.


commit b8f92a1279024c2f6a3b113cc3855e3a380957bf
Merge: 452fbf3 61985a3
Author: Sascha Steinbiss <[email protected]>
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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[med-svn] [ariba] 02/03: Merge tag 'upstream/2.2.0+ds'

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