[med-svn] [ariba] branch upstream updated (74d1bf9 -> 7e09fda)
Sascha Steinbiss
satta at debian.org
Sun Jul 31 21:39:03 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 74d1bf9 Imported Upstream version 1.0.1
new 7e09fda Imported Upstream version 2.0.0+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:
.gitignore | 6 +
.travis.yml | 3 -
README.md | 28 +-
ariba/__init__.py | 3 +
ariba/aln_to_metadata.py | 31 +-
ariba/assembly.py | 58 +-
ariba/assembly_compare.py | 13 +-
ariba/assembly_variants.py | 27 +-
ariba/cdhit.py | 164 +-
ariba/cluster.py | 81 +-
ariba/clusters.py | 295 +-
ariba/ext/fml-asm_ariba.cpp | 194 +
ariba/ext/minimap_ariba.cpp | 351 ++
ariba/external_progs.py | 25 +-
ariba/flag.py | 2 +-
ariba/histogram.py | 13 +-
ariba/mash.py | 67 +
ariba/read_filter.py | 83 +
ariba/read_store.py | 33 +-
ariba/ref_genes_getter.py | 103 +-
ariba/ref_preparer.py | 161 +-
ariba/refdata_query.py | 89 +
ariba/reference_data.py | 395 +-
ariba/report.py | 78 +-
ariba/report_filter.py | 19 +-
ariba/sequence_metadata.py | 25 +-
ariba/summary.py | 45 +-
ariba/summary_cluster.py | 8 +-
ariba/tasks/__init__.py | 14 +
ariba/tasks/aln2meta.py | 16 +-
ariba/tasks/flag.py | 8 +-
ariba/tasks/getref.py | 13 +-
ariba/tasks/prepareref.py | 36 +-
ariba/tasks/refquery.py | 7 +
ariba/tasks/reportfilter.py | 17 +-
ariba/tasks/run.py | 47 +-
ariba/tasks/summary.py | 33 +-
ariba/tasks/test.py | 16 +-
ariba/tasks/version.py | 2 +-
ariba/test_run_data/metadata.tsv | 33 +-
ariba/test_run_data/non_coding.fa | 10 -
ariba/test_run_data/presence_absence.fa | 5 -
ariba/test_run_data/reads_1.fq | 2542 ++++++---
ariba/test_run_data/reads_2.fq | 2542 ++++++---
.../test_run_data/ref_fasta_to_make_reads_from.fa | 42 +-
ariba/test_run_data/ref_seqs.fa | 27 +
ariba/test_run_data/variants_only.fa | 6 -
ariba/tests/aln_to_metadata_test.py | 46 +-
ariba/tests/assembly_compare_test.py | 7 +-
ariba/tests/assembly_test.py | 83 +-
ariba/tests/assembly_variants_test.py | 87 +-
ariba/tests/bam_parse_test.py | 2 -
ariba/tests/cdhit_test.py | 128 +-
ariba/tests/cluster_test.py | 140 +-
ariba/tests/clusters_test.py | 167 +-
.../data/aln_to_metadata_make_cluster_file.out | 2 +-
.../data/aln_to_metadata_run_coding.out.cluster | 2 +-
.../tests/data/aln_to_metadata_run_coding.out.tsv | 14 +-
.../data/aln_to_metadata_run_noncoding.out.cluster | 2 +-
.../data/aln_to_metadata_run_noncoding.out.tsv | 14 +-
.../assembly_assemble_with_fermilite.expected.fa | 2 +
.../assembly_assemble_with_fermilite.expected.log | 11 +
.../assembly_assemble_with_fermilite.reads_1.fq | 232 +
.../assembly_assemble_with_fermilite.reads_2.fq | 232 +
...mbly_assemble_with_fermilite_fails.expected.log | 11 +
...sembly_assemble_with_fermilite_fails.reads_1.fq | 4 +
...sembly_assemble_with_fermilite_fails.reads_2.fq | 4 +
.../tests/data/assembly_run_fermilite.expected.fa | 2 +
.../tests/data/assembly_run_fermilite.expected.log | 10 +
ariba/tests/data/assembly_run_fermilite.reads.fq | 464 ++
.../data/assembly_run_fermilite_fail.reads.fq | 4 +
.../data/assembly_run_fermilite_fails.expected.log | 10 +
..._one_variant_for_one_contig_coding_metadata.tsv | 15 +-
..._variant_for_one_contig_non_coding.metadata.tsv | 14 +-
ariba/tests/data/cdhit_test_fake_run.out.fa | 40 -
.../data/cdhit_test_get_clusters_from_bak_file.in | 5 +
ariba/tests/data/cdhit_test_get_ids.fa | 6 -
.../data/cdhit_test_parse_cluster_info_file.infile | 6 -
.../data/cdhit_test_rename_clusters.expected.fa | 6 -
ariba/tests/data/cdhit_test_rename_clusters.in.fa | 6 -
ariba/tests/data/cdhit_test_run.out.fa | 20 -
.../cdhit_test_run_get_clusters_from_dict.out.fa | 4 -
...a => cluster_test_full_run_assembly_fail.in.fa} | 0
.../cluster_test_full_run_assembly_fail.in.tsv | 1 +
...=> cluster_test_full_run_choose_ref_fail.in.fa} | 2 +-
.../cluster_test_full_run_choose_ref_fail.in.tsv | 2 +
...st_full_run_choose_ref_fail.presence_absence.fa | 2 -
.../reads_1.fq | 214 +-
.../reads_2.fq | 214 +-
...r_test_full_run_no_reads_after_filtering.in.fa} | 0
...r_test_full_run_no_reads_after_filtering.in.tsv | 1 +
.../reads_1.fq | 4 +
.../reads_2.fq | 4 +
.../references.fa | 0
...luster_test_full_run_ok_gene_start_mismatch.fa} | 4 +-
...st_full_run_ok_gene_start_mismatch.metadata.tsv | 1 +
...run_ok_gene_start_mismatch.ref_to_make_reads.fa | 7 +
.../reads_1.fq | 224 +
.../reads_2.fq | 224 +
.../references.fa | 4 +-
...luster_test_full_run_ok_non_coding.metadata.tsv | 11 +-
..._test_full_run_ok_presence_absence.metadata.tsv | 9 +-
...nts_only.not_present.always_report.metadata.tsv | 5 +-
...l_run_ok_variants_only.not_present.metadata.tsv | 5 +-
..._full_run_ok_variants_only.present.metadata.tsv | 7 +-
ariba/tests/data/cluster_test_init_refdata.tsv | 1 +
...luster_test_number_of_reads_for_assembly.ref.fa | 3 -
.../data/clusters_test_bam_to_clusters_reads.bam | Bin 453 -> 0 bytes
.../data/clusters_test_bam_to_clusters_reads.db.fa | 54 -
...usters_test_bam_to_clusters_reads.read_store.gz | Bin 213 -> 0 bytes
.../clusters_test_bam_to_clusters_reads.reads_1.fq | 8 -
.../clusters_test_bam_to_clusters_reads.reads_2.fq | 8 -
...ers_test_bam_to_clusters_reads_no_reads_map.bam | Bin 364 -> 0 bytes
...rs_test_bam_to_clusters_reads_no_reads_map_1.fq | 8 -
...rs_test_bam_to_clusters_reads_no_reads_map_2.fq | 8 -
ariba/tests/data/clusters_test_dummy_db.tsv | 1 +
..._test_load_minimap_files.cluster2representative | 2 +
.../clusters_test_load_minimap_files.clusterCounts | 2 +
...lusters_test_load_minimap_files.insertHistogram | 7 +
.../clusters_test_load_minimap_files.properPairs | 1 +
.../clusters_test_load_minimap_insert_histogram.in | 7 +
...test_load_minimap_out_cluster2representative.in | 2 +
...lusters_test_load_minimap_out_cluster_counts.in | 2 +
.../clusters_test_load_minimap_proper_pairs.in | 1 +
.../{info.txt => 00.info.txt} | 0
.../01.filter.check_metadata.tsv | 3 +
.../02.cdhit.all.fa | 6 +
.../02.cdhit.clusters.pickle | Bin 0 -> 135 bytes
.../cdhit.clusters.pickle | Bin 34 -> 0 bytes
.../refcheck.01.check_variants.non_coding.fa | 2 -
.../refcheck.01.check_variants.presence_absence.fa | 2 -
.../refcheck.01.check_variants.tsv | 2 -
.../refcheck.01.check_variants.variants_only.fa | 2 -
...test_minimap_reads_to_all_ref_seqs.clusters.tsv | 3 +
...eads_to_all_ref_seqs.out.cluster2representative | 2 +
...minimap_reads_to_all_ref_seqs.out.clusterCounts | 2 +
...nimap_reads_to_all_ref_seqs.out.insertHistogram | 31 +
...t_minimap_reads_to_all_ref_seqs.out.properPairs | 1 +
...s_test_minimap_reads_to_all_ref_seqs.reads_1.fq | 5884 ++++++++++++++++++++
...s_test_minimap_reads_to_all_ref_seqs.reads_2.fq | 5884 ++++++++++++++++++++
...sters_test_minimap_reads_to_all_ref_seqs.ref.fa | 545 ++
ariba/tests/data/clusters_test_write_report.tsv | 2 +-
ariba/tests/data/mash_test_run.in.qry.fa | 10 +
ariba/tests/data/mash_test_run.in.ref.fa | 40 +
.../data/read_filter_cdhit_clstr_to_reads.in.clstr | 18 +
.../data/read_filter_test_run.expected.reads_1.fq | 24 +
.../data/read_filter_test_run.expected.reads_2.fq | 24 +
.../tests/data/read_filter_test_run.in.read_store | 38 +
.../tests/data/read_filter_test_run.in.reads_1.fq | 72 +
.../tests/data/read_filter_test_run.in.reads_2.fq | 72 +
ariba/tests/data/read_filter_test_run.in.ref.fa | 54 +
...ead_filter_test_run_cdhit_est_2d.expected.clstr | 42 +
.../read_filter_test_run_cdhit_est_2d.reads.in.fa | 108 +
.../read_filter_test_run_cdhit_est_2d.ref.in.fa | 54 +
.../read_store_test_get_reads.expected.reads.fa | 12 +
...=> read_store_test_get_reads.expected.reads.fq} | 12 +
.../read_store_test_get_reads.expected.reads_1.fa | 6 +
... read_store_test_get_reads.expected.reads_1.fq} | 0
.../read_store_test_get_reads.expected.reads_2.fa | 6 +
... read_store_test_get_reads.expected.reads_2.fq} | 0
...tore_test_get_reads.expected.reads_subset.1.fq} | 4 -
...tore_test_get_reads.expected.reads_subset.2.fq} | 4 -
ariba/tests/data/ref_preparer_test_run.in.1.fa | 8 +
ariba/tests/data/ref_preparer_test_run.in.1.tsv | 4 +
ariba/tests/data/ref_preparer_test_run.in.2.fa | 8 +
ariba/tests/data/ref_preparer_test_run.in.2.tsv | 5 +
ariba/tests/data/ref_preparer_test_run.in.3.fa | 2 +
.../data/ref_preparer_test_run.out/00.info.txt | 6 +
.../ref_preparer_test_run.out/00.version_info.txt | 5 +
.../01.filter.check_genes.log | 5 +
.../01.filter.check_metadata.log | 1 +
.../01.filter.check_metadata.tsv | 8 +
.../data/ref_preparer_test_run.out/02.cdhit.all.fa | 16 +
.../02.cdhit.clusters.pickle | Bin 0 -> 276 bytes
.../02.cdhit.clusters.tsv | 5 +
.../ref_preparer_test_run.out/02.cdhit.gene.fa | 6 +
.../02.cdhit.gene.varonly.fa | 2 +
.../02.cdhit.noncoding.fa | 8 +
.../02.cdhit.noncoding.varonly.fa} | 0
.../data/ref_preparer_test_write_info_file.out | 5 -
ariba/tests/data/refdata_query_prepareref.in.fa | 82 +
ariba/tests/data/refdata_query_prepareref.in.tsv | 13 +
.../data/refdata_query_prepareref/00.info.txt | 3 +
.../data/refdata_query_prepareref/00.rename_info | 1 +
.../refdata_query_prepareref/00.version_info.txt | 32 +
.../01.filter.check_genes.log | 6 +
.../01.filter.check_metadata.log} | 0
.../01.filter.check_metadata.tsv | 13 +
.../data/refdata_query_prepareref/02.cdhit.all.fa | 82 +
.../02.cdhit.clusters.pickle | Bin 0 -> 314 bytes
.../refdata_query_prepareref/02.cdhit.clusters.tsv | 6 +
.../data/refdata_query_prepareref/02.cdhit.gene.fa | 46 +
.../02.cdhit.gene.varonly.fa | 18 +
.../refdata_query_prepareref/02.cdhit.noncoding.fa | 14 +
.../02.cdhit.noncoding.varonly.fa | 4 +
...reference_data_filter_bad_data.expected.all.fa} | 4 +
...ata_filter_bad_data.expected.check_metadata.log | 5 +
...ata_filter_bad_data.expected.check_metadata.tsv | 10 +
.../reference_data_filter_bad_data.expected.log | 5 +
...ence_data_filter_bad_data.expected.metadata.tsv | 10 +
.../data/reference_data_filter_bad_data.in.fa | 12 +
...ence_data_filter_bad_data_metadata.expected.tsv | 9 -
.../reference_data_filter_bad_data_metadata.in.tsv | 37 +-
...nce_data_filter_bad_data_non_coding.expected.fa | 2 -
..._data_filter_bad_data_variants_only.expected.fa | 2 -
ariba/tests/data/reference_data_get_filename | 1 -
ariba/tests/data/reference_data_init.tsv | 4 -
.../data/reference_data_init_fails.empty.fa} | 0
.../data/reference_data_init_fails.empty.tsv} | 0
ariba/tests/data/reference_data_init_fails.in.fa | 4 +
...nce_absence.fa => reference_data_init_ok.in.fa} | 2 +-
ariba/tests/data/reference_data_init_ok.in.tsv | 2 +
...fa => reference_data_load_all_fasta_files.in.1} | 0
.../data/reference_data_load_all_fasta_files.in.2 | 2 +
.../reference_data_load_all_metadata_tsvs.1.tsv | 1 +
.../reference_data_load_all_metadata_tsvs.2.tsv | 2 +
...ad_input_files_and_check_seq_names.bad.in.csv.1 | 1 +
...ad_input_files_and_check_seq_names.bad.in.csv.2 | 2 +
...oad_input_files_and_check_seq_names.bad.in.fa.1 | 4 +
...oad_input_files_and_check_seq_names.bad.in.fa.2 | 2 +
...d_input_files_and_check_seq_names.good.in.csv.1 | 1 +
...d_input_files_and_check_seq_names.good.in.csv.2 | 2 +
...d_input_files_and_check_seq_names.good.in.fa.1} | 0
...ad_input_files_and_check_seq_names.good.in.fa.2 | 2 +
.../data/reference_data_load_metadata_tsv.tsv | 6 +-
.../reference_data_make_catted_fasta.expected.fa | 6 -
.../reference_data_make_catted_fasta.noncoding.fa | 2 -
...ence_data_make_catted_fasta.presence_absence.fa | 2 -
...ference_data_make_catted_fasta.variants_only.fa | 2 -
.../data/reference_data_remove_bad_genes.in.fa | 2 +
.../data/reference_data_remove_bad_genes.in.tsv | 6 +
.../tests/data/reference_data_rename_sequences.fa | 22 +
.../reference_data_rename_sequences.noncoding.fa | 4 -
...rence_data_rename_sequences.presence_absence.fa | 10 -
...eference_data_rename_sequences.variants_only.fa | 8 -
.../reference_data_rename_sequences_metadata.tsv | 22 +-
ariba/tests/data/reference_data_sequence.in.fa | 4 +
ariba/tests/data/reference_data_sequence.in.tsv | 2 +
.../reference_data_sequence.presence_absence.fa | 2 -
...erence_data_sequence_length.presence_absence.fa | 2 -
.../tests/data/reference_data_sequence_type.in.fa | 8 +
.../tests/data/reference_data_sequence_type.in.tsv | 4 +
.../data/reference_data_sequence_type.noncoding.fa | 2 -
...eference_data_sequence_type.presence_absence.fa | 2 -
.../reference_data_sequence_type.variants_only.fa | 2 -
...nce_data_test_all_non_wild_type_variants.ref.fa | 6 +
...est_all_non_wild_type_variants.ref.noncoding.fa | 2 -
...test_all_non_wild_type_variants.ref.pres_abs.fa | 2 -
...test_all_non_wild_type_variants.ref.var_only.fa | 2 -
...erence_data_test_all_non_wild_type_variants.tsv | 20 +-
...rence_data_test_cluster_with_cdhit.clusters.tsv | 3 -
...a_test_cluster_with_cdhit.expected.clusters.tsv | 3 +
..._cluster_with_cdhit.expected_representatives.fa | 10 -
...> reference_data_test_cluster_with_cdhit.in.fa} | 5 +
.../reference_data_test_cluster_with_cdhit.in.tsv | 5 +
...ence_data_test_cluster_with_cdhit.non_coding.fa | 5 -
...ata_test_cluster_with_cdhit.presence_absence.fa | 10 -
...st_cluster_with_cdhit_clusters_in_file.clusters | 4 -
...luster_with_cdhit_clusters_in_file.clusters.tsv | 4 -
...th_cdhit_clusters_in_file.expected.clusters.tsv | 4 +
...ter_with_cdhit_clusters_in_file.in.clusters.tsv | 4 +
...test_cluster_with_cdhit_clusters_in_file.in.fa} | 12 +-
...cluster_with_cdhit_clusters_in_file.in.meta.tsv | 6 +
...uster_with_cdhit_clusters_in_file.non_coding.fa | 10 -
..._test_cluster_with_cdhit_nocluster.clusters.tsv | 6 -
...ster_with_cdhit_nocluster.expected.clusters.tsv | 6 +
...e_data_test_cluster_with_cdhit_nocluster.in.fa} | 20 +-
...e_data_test_cluster_with_cdhit_nocluster.in.tsv | 6 +
...test_cluster_with_cdhit_nocluster.non_coding.fa | 10 -
...luster_with_cdhit_nocluster.presence_absence.fa | 10 -
...ata_test_write_cluster_allocation_file.expected | 8 +-
.../reference_data_test_write_seqs_to_fasta.in.tsv | 5 +
.../data/reference_data_write_dict_of_sequences.fa | 4 -
.../reference_data_write_metadata_tsv.expected.tsv | 4 +-
.../data/reference_data_write_metadata_tsv.tsv | 4 +-
...nce_data_write_metadata_tsv_presence_absence.fa | 4 -
.../reference_data_write_sequences_to_files.all.fa | 10 +
...reference_data_write_sequences_to_files.gene.fa | 2 +
...e_data_write_sequences_to_files.gene.varonly.fa | 2 +
...ence_data_write_sequences_to_files.noncoding.fa | 4 +
...a_write_sequences_to_files.noncoding.varonly.fa | 2 +
ariba/tests/data/report_filter_test_init_good.tsv | 10 +-
.../data/report_filter_test_load_report_good.tsv | 10 +-
.../tests/data/report_filter_test_run.expected.tsv | 12 +-
ariba/tests/data/report_filter_test_run.in.tsv | 18 +-
.../tests/data/report_filter_test_write_report.tsv | 8 +-
.../summary_sample_test_column_names_tuples.tsv | 16 +-
.../summary_sample_test_column_summary_data.tsv | 16 +-
.../data/summary_sample_test_load_file.in.tsv | 14 +-
.../tests/data/summary_sample_test_var_groups.tsv | 14 +-
.../data/summary_test_gather_output_rows.in.1.tsv | 6 +-
.../data/summary_test_gather_output_rows.in.2.tsv | 10 +-
.../data/summary_test_get_all_cluster_names.1.tsv | 6 +-
.../data/summary_test_get_all_cluster_names.2.tsv | 10 +-
.../data/summary_test_get_all_var_groups.1.tsv | 6 +-
.../data/summary_test_get_all_var_groups.2.tsv | 10 +-
.../tests/data/summary_test_load_input_files.1.tsv | 6 +-
.../tests/data/summary_test_load_input_files.2.tsv | 10 +-
.../summary_test_newick_from_dist_matrix.distances | 8 +-
.../data/summary_test_newick_from_dist_matrix.tre | 1 -
.../summary_test_write_distance_matrix.distances | 8 +-
ariba/tests/data/vfdb_parser_test_run.out.tsv | 5 +-
ariba/tests/external_progs_test.py | 3 +-
ariba/tests/flag_test.py | 2 +-
ariba/tests/histogram_test.py | 4 +-
ariba/tests/link_test.py | 7 +-
ariba/tests/mapping_test.py | 1 -
ariba/tests/mash_test.py | 21 +
ariba/tests/read_filter_test.py | 54 +
ariba/tests/read_store_test.py | 70 +-
ariba/tests/ref_preparer_test.py | 162 +-
ariba/tests/reference_data_test.py | 684 +--
ariba/tests/report_filter_test.py | 65 +-
ariba/tests/samtools_variants_test.py | 2 -
ariba/tests/scaffold_graph_test.py | 9 +-
ariba/tests/sequence_metadata_test.py | 46 +-
ariba/tests/sequence_variant_test.py | 2 +-
ariba/tests/summary_cluster_test.py | 211 +-
ariba/tests/summary_sample_test.py | 6 +-
ariba/tests/summary_test.py | 54 +-
ariba/tests/test_refdata_query.py | 90 +
ariba/tests/vfdb_parser_test.py | 10 +-
ariba/versions.py | 6 +-
ariba/vfdb_parser.py | 9 +-
install_dependencies.sh | 35 +-
scripts/ariba | 226 +-
setup.py | 52 +-
327 files changed, 22518 insertions(+), 4052 deletions(-)
create mode 100644 ariba/ext/fml-asm_ariba.cpp
create mode 100644 ariba/ext/minimap_ariba.cpp
create mode 100644 ariba/mash.py
create mode 100644 ariba/read_filter.py
create mode 100644 ariba/refdata_query.py
create mode 100644 ariba/tasks/refquery.py
delete mode 100644 ariba/test_run_data/non_coding.fa
delete mode 100644 ariba/test_run_data/presence_absence.fa
create mode 100644 ariba/test_run_data/ref_seqs.fa
delete mode 100644 ariba/test_run_data/variants_only.fa
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite.expected.fa
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite.expected.log
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq
create mode 100644 ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq
create mode 100644 ariba/tests/data/assembly_run_fermilite.expected.fa
create mode 100644 ariba/tests/data/assembly_run_fermilite.expected.log
create mode 100644 ariba/tests/data/assembly_run_fermilite.reads.fq
create mode 100644 ariba/tests/data/assembly_run_fermilite_fail.reads.fq
create mode 100644 ariba/tests/data/assembly_run_fermilite_fails.expected.log
delete mode 100644 ariba/tests/data/cdhit_test_fake_run.out.fa
create mode 100644 ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in
delete mode 100644 ariba/tests/data/cdhit_test_get_ids.fa
delete mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.infile
delete mode 100644 ariba/tests/data/cdhit_test_rename_clusters.expected.fa
delete mode 100644 ariba/tests/data/cdhit_test_rename_clusters.in.fa
delete mode 100644 ariba/tests/data/cdhit_test_run.out.fa
delete mode 100644 ariba/tests/data/cdhit_test_run_get_clusters_from_dict.out.fa
copy ariba/tests/data/{cluster_test_full_run_assembly_fail.noncoding.fa => cluster_test_full_run_assembly_fail.in.fa} (100%)
create mode 100644 ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv
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