[med-svn] [ariba] branch upstream updated (a8ce3c5 -> 194d86c)
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 14:13:05 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch upstream
in repository ariba.
from a8ce3c5 Imported Upstream version 0.6.0
new 194d86c Imported Upstream version 1.0.0
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:
.travis.yml | 23 +
README.md | 67 +-
ariba/__init__.py | 28 +-
ariba/aln_to_metadata.py | 269 ++++
ariba/assembly.py | 377 ++++++
ariba/assembly_compare.py | 371 ++++++
ariba/assembly_variants.py | 323 +++++
ariba/best_seq_chooser.py | 98 ++
ariba/card_record.py | 111 ++
ariba/cdhit.py | 199 +--
ariba/cluster.py | 1319 +++++---------------
ariba/clusters.py | 674 ++++++----
ariba/common.py | 31 +-
ariba/external_progs.py | 224 ++--
ariba/faidx.py | 5 +-
ariba/flag.py | 9 +-
ariba/mapping.py | 196 +--
ariba/read_store.py | 60 +
ariba/ref_genes_getter.py | 267 ++++
ariba/ref_preparer.py | 189 +++
ariba/refcheck.py | 90 --
ariba/reference_data.py | 510 ++++++++
ariba/report.py | 268 ++++
ariba/report_filter.py | 216 ++++
ariba/samtools_variants.py | 194 +++
ariba/sequence_metadata.py | 48 +
ariba/sequence_variant.py | 70 ++
ariba/summary.py | 480 ++++---
ariba/summary_cluster.py | 258 ++++
ariba/summary_sample.py | 61 +
ariba/tasks/aln2meta.py | 28 +
ariba/tasks/getref.py | 19 +
ariba/tasks/prepareref.py | 59 +
ariba/tasks/refcheck.py | 31 -
ariba/tasks/reportfilter.py | 35 +
ariba/tasks/run.py | 90 +-
ariba/tasks/summary.py | 108 +-
ariba/tasks/test.py | 94 ++
ariba/tasks/version.py | 6 +-
ariba/test_run_data/metadata.tsv | 14 +
ariba/test_run_data/non_coding.fa | 10 +
ariba/test_run_data/presence_absence.fa | 5 +
ariba/test_run_data/reads_1.fq | 908 ++++++++++++++
ariba/test_run_data/reads_2.fq | 908 ++++++++++++++
.../test_run_data/ref_fasta_to_make_reads_from.fa | 36 +
ariba/test_run_data/variants_only.fa | 6 +
ariba/tests/aln_to_metadata_test.py | 411 ++++++
ariba/tests/assembly_compare_test.py | 381 ++++++
ariba/tests/assembly_test.py | 135 ++
ariba/tests/assembly_variants_test.py | 385 ++++++
ariba/tests/best_seq_chooser_test.py | 69 +
ariba/tests/card_record_test.py | 205 +++
ariba/tests/cdhit_test.py | 130 +-
ariba/tests/cluster_test.py | 967 +++-----------
ariba/tests/clusters_test.py | 199 ++-
ariba/tests/common_test.py | 22 +
.../tests/data/aln_to_metadata_load_aln_file.in.fa | 4 +
.../data/aln_to_metadata_load_vars_file_bad.1.tsv | 2 +
.../data/aln_to_metadata_load_vars_file_bad.2.tsv | 2 +
.../data/aln_to_metadata_load_vars_file_good.tsv | 3 +
.../data/aln_to_metadata_make_cluster_file.out | 1 +
ariba/tests/data/aln_to_metadata_run_coding.in.fa | 10 +
ariba/tests/data/aln_to_metadata_run_coding.in.tsv | 2 +
.../data/aln_to_metadata_run_coding.out.cluster | 1 +
ariba/tests/data/aln_to_metadata_run_coding.out.fa | 10 +
.../tests/data/aln_to_metadata_run_coding.out.tsv | 7 +
.../tests/data/aln_to_metadata_run_noncoding.in.fa | 10 +
.../data/aln_to_metadata_run_noncoding.in.tsv | 2 +
.../data/aln_to_metadata_run_noncoding.out.cluster | 1 +
.../data/aln_to_metadata_run_noncoding.out.fa | 10 +
.../data/aln_to_metadata_run_noncoding.out.tsv | 7 +
...ssembly_compare_parse_nucmer_coords_file.coords | 7 +
... assembly_test_assemble_with_spades_reads_1.fq} | 0
... assembly_test_assemble_with_spades_reads_2.fq} | 0
...a => assembly_test_assemble_with_spades_ref.fa} | 0
.../assembly_test_check_spades_log_file.log.bad | 5 +
.../assembly_test_check_spades_log_file.log.good | 5 +
... => assembly_test_fix_contig_orientation.in.fa} | 7 +
...=> assembly_test_fix_contig_orientation.out.fa} | 7 +
...=> assembly_test_fix_contig_orientation.ref.fa} | 0
...st_gapfill_with_gapfiller.scaffolds_no_gaps.fa} | 0
..._gapfill_with_gapfiller.scaffolds_with_gaps.fa} | 0
...ssembly_test_gapfill_with_gapfiller_reads_1.fq} | 0
...ssembly_test_gapfill_with_gapfiller_reads_2.fq} | 0
.../assembly_test_has_gaps_to_fill.has_gaps.fa | 2 +
.../data/assembly_test_has_gaps_to_fill.no_gaps.fa | 4 +
...> assembly_test_parse_assembly_bam.assembly.fa} | 0
...am.bam => assembly_test_parse_assembly_bam.bam} | Bin
....in.fa => assembly_test_rename_scaffolds.in.fa} | 0
.../data/assembly_test_rename_scaffolds.out.fa | 6 +
... assembly_test_scaffold_with_sspace_contigs.fa} | 0
... assembly_test_scaffold_with_sspace_reads_1.fq} | 0
... assembly_test_scaffold_with_sspace_reads_2.fq} | 0
... => assembly_test_set_assembly_kmer_reads_1.fq} | 0
... => assembly_test_set_assembly_kmer_reads_2.fq} | 0
...ly_variants_test_get_mummer_variants.none.snps} | 0
...bly_variants_test_get_mummer_variants.snp.snps} | 0
..._one_variant_for_one_contig_coding_metadata.tsv | 11 +
...riant_for_one_contig_coding_presence_absence.fa | 2 +
..._variant_for_one_contig_non_coding.metadata.tsv | 11 +
...sembly_variants_test_get_variants_non_coding.fa | 2 +
..._variants_test_get_variants_presence_absence.fa | 2 +
...ariants_test_get_variants_presence_absence.snps | 3 +
...bly_variants_test_get_variants_variants_only.fa | 2 +
...y_variants_test_get_variants_variants_only.snps | 3 +
...s_1.fq => best_seq_chooser_best_seq_reads_1.fq} | 0
...s_2.fq => best_seq_chooser_best_seq_reads_2.fq} | 0
.../genes.fa => best_seq_chooser_best_seq_ref.fa} | 0
.../data/best_seq_chooser_best_seq_ref.fa.fai | 3 +
...ser_get_best_seq_by_alignment_score_reads_1.fq} | 0
...ser_get_best_seq_by_alignment_score_reads_2.fq} | 0
...chooser_get_best_seq_by_alignment_score_ref.fa} | 0
...oser_get_best_seq_by_alignment_score_ref.fa.fai | 3 +
...t_seq_chooser_total_alignment_score_reads_1.fq} | 0
...t_seq_chooser_total_alignment_score_reads_2.fq} | 0
..._seq_chooser_total_alignment_score_ref_seqs.fa} | 0
...q_chooser_total_alignment_score_ref_seqs.fa.fai | 3 +
ariba/tests/data/cdhit_test_enumerate_fasta.in.fa | 6 -
ariba/tests/data/cdhit_test_enumerate_fasta.out.fa | 6 -
ariba/tests/data/cdhit_test_fake_run.out.fa | 8 +-
.../data/cdhit_test_load_user_clusters_file.bad1 | 1 +
.../data/cdhit_test_load_user_clusters_file.bad2 | 2 +
.../data/cdhit_test_load_user_clusters_file.bad3 | 2 +
.../data/cdhit_test_load_user_clusters_file.good | 3 +
.../data/cdhit_test_parse_cluster_info_file.in.fa | 40 -
...dhit_test_parse_cluster_info_file.in.renamed.fa | 40 -
.../data/cdhit_test_parse_cluster_info_file.infile | 6 +
.../data/cdhit_test_parse_cluster_info_file.out.fa | 20 -
...t_test_parse_cluster_info_file.out.fa.bak.clstr | 4 -
.../data/cdhit_test_rename_clusters.expected.fa | 6 +
ariba/tests/data/cdhit_test_rename_clusters.in.fa | 6 +
ariba/tests/data/cdhit_test_rename_fasta.in.fa | 6 -
ariba/tests/data/cdhit_test_run.out.fa | 4 +-
...hit_test_run_get_clusters_from_dict.in.clusters | 2 +
...=> cdhit_test_run_get_clusters_from_dict.in.fa} | 6 +-
.../cdhit_test_run_get_clusters_from_dict.out.fa | 4 +
.../cluster_test_assemble_with_spades/genes.fa | 2 -
.../data/cluster_test_choose_best_gene.gene.fa | 6 -
ariba/tests/data/cluster_test_count_reads_1.fq | 8 +
ariba/tests/data/cluster_test_count_reads_2.fq | 8 +
.../cluster_test_fix_contig_orientation/genes.fa | 10 -
...luster_test_full_run_assembly_fail.noncoding.fa | 8 +
.../cluster_test_full_run_assembly_fail/reads_1.fq | 8 +
.../cluster_test_full_run_assembly_fail/reads_2.fq | 8 +
.../references.fa | 8 +
...st_full_run_choose_ref_fail.presence_absence.fa | 2 +
.../reads_1.fq | 4 +
.../reads_2.fq | 4 +
.../references.fa | 4 +
.../data/cluster_test_full_run_ok_non_coding.fa | 6 +
...luster_test_full_run_ok_non_coding.metadata.tsv | 5 +
.../cluster_test_full_run_ok_non_coding/reads_1.fq | 144 +++
.../cluster_test_full_run_ok_non_coding/reads_2.fq | 144 +++
.../references.fa | 6 +
.../cluster_test_full_run_ok_presence_absence.fa | 5 +
..._test_full_run_ok_presence_absence.metadata.tsv | 4 +
.../reads_1.fq | 128 ++
.../reads_2.fq | 128 ++
.../references.fa | 5 +
.../data/cluster_test_full_run_ok_variants_only.fa | 5 +
...nts_only.not_present.always_report.metadata.tsv | 2 +
...l_run_ok_variants_only.not_present.metadata.tsv | 2 +
..._full_run_ok_variants_only.present.metadata.tsv | 3 +
.../reads_1.fq | 132 ++
.../reads_2.fq | 132 ++
.../references.fa | 5 +
.../cluster_test_gapfill_with_gapfiller.gene.fa | 2 -
.../cluster_test_gapfill_with_gapfiller/genes.fa | 2 -
ariba/tests/data/cluster_test_generic/genes.fa | 2 -
ariba/tests/data/cluster_test_generic/reads_1.fq | 4 -
ariba/tests/data/cluster_test_generic/reads_2.fq | 4 -
.../data/cluster_test_get_read_counts/genes.fa | 2 -
.../data/cluster_test_get_read_counts/reads_1.fq | 4 -
.../data/cluster_test_get_read_counts/reads_2.fq | 4 -
.../cluster_test_get_read_counts_fail/genes.fa | 2 -
.../cluster_test_get_read_counts_fail/reads_1.fq | 8 -
.../cluster_test_get_read_counts_fail/reads_2.fq | 4 -
.../reads_1.fq | 0
.../reads_2.fq | 0
ariba/tests/data/cluster_test_init_refdata.fa | 2 +
.../cluster_test_load_final_contigs.contigs.fa | 6 -
.../data/cluster_test_load_final_contigs/genes.fa | 2 -
.../cluster_test_load_final_contigs/reads_1.fq | 4 -
.../cluster_test_load_final_contigs/reads_2.fq | 4 -
.../cluster_test_make_reads_for_assembly.in1.fq | 40 +
.../cluster_test_make_reads_for_assembly.in2.fq | 40 +
.../cluster_test_make_reads_for_assembly.out1.fq | 28 +
.../cluster_test_make_reads_for_assembly.out2.fq | 28 +
.../cluster_test_make_report_lines.read_depths.gz | Bin 78 -> 0 bytes
...uster_test_make_report_lines.read_depths.gz.tbi | Bin 91 -> 0 bytes
...its_to_assembled_gene_sequences.expected.out.fa | 7 -
...luster_test_number_of_reads_for_assembly.ref.fa | 3 +
.../data/cluster_test_parse_assembly_bam/genes.fa | 2 -
.../cluster_test_parse_assembly_bam/reads_1.fq | 4 -
.../cluster_test_parse_assembly_bam/reads_2.fq | 4 -
...uster_test_parse_assembly_vs_gene_coords.coords | 7 -
.../genes.fa | 2 -
.../reads_1.fq | 4 -
.../reads_2.fq | 4 -
.../data/cluster_test_rename_scaffolds.out.fa | 6 -
.../data/cluster_test_rename_scaffolds/genes.fa | 2 -
.../data/cluster_test_rename_scaffolds/reads_1.fq | 4 -
.../data/cluster_test_rename_scaffolds/reads_2.fq | 4 -
.../data/cluster_test_scaffold_with_sspace.gene.fa | 2 -
.../cluster_test_scaffold_with_sspace/genes.fa | 2 -
.../data/cluster_test_set_assembly_kmer/genes.fa | 2 -
.../data/cluster_test_set_assembly_kmer/reads_1.fq | 12 -
.../data/cluster_test_set_assembly_kmer/reads_2.fq | 12 -
...usters_test_bam_to_clusters.out.ref2.reads_1.fq | 4 -
...usters_test_bam_to_clusters.out.ref2.reads_2.fq | 4 -
.../clusters_test_bam_to_clusters_reads.db.fa.fai | 3 +
...usters_test_bam_to_clusters_reads.read_store.gz | Bin 0 -> 213 bytes
...ers_test_bam_to_clusters_reads_no_reads_map.bam | Bin 0 -> 364 bytes
...s_test_bam_to_clusters_reads_no_reads_map_1.fq} | 4 +-
...s_test_bam_to_clusters_reads_no_reads_map_2.fq} | 4 +-
ariba/tests/data/clusters_test_dummy_db.fa | 2 +
ariba/tests/data/clusters_test_load_data_info_file | 5 +
.../cdhit.clusters.pickle | Bin 0 -> 34 bytes
.../info.txt | 5 +
.../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 +
...te_catted_assembled_genes_fasta.expected.out.fa | 10 +-
..._write_catted_assembled_genes_fasta.in.gene1.fa | 4 -
..._write_catted_assembled_genes_fasta.in.gene2.fa | 2 -
...atted_genes_matching_refs_fasta.expected.out.fa | 4 +
ariba/tests/data/clusters_test_write_report.tsv | 6 +-
...ing_test_bowtie2_remove_both_unmapped_reads.bam | Bin 0 -> 422 bytes
...ng_test_bowtie2_remove_both_unmapped_reads_1.fq | 16 +
...ng_test_bowtie2_remove_both_unmapped_reads_2.fq | 16 +
...ert.bam => mapping_test_sam_pair_to_insert.bam} | Bin
..._to_fastq.bam => mapping_test_sam_to_fastq.bam} | Bin
ariba/tests/data/mapping_test_smalt_reads_1.fq | 28 -
ariba/tests/data/mapping_test_smalt_reads_2.fq | 28 -
ariba/tests/data/mapping_test_smalt_ref.fa | 5 -
ariba/tests/data/mapping_test_smalt_ref.fa.fai | 1 -
ariba/tests/data/mapping_test_smalt_sorted.bam | Bin 648 -> 0 bytes
ariba/tests/data/mapping_test_smalt_unsorted.bam | Bin 656 -> 0 bytes
ariba/tests/data/read_store_test_clean.in | 10 +
.../read_store_test_compress_and_index_file.in | 10 +
ariba/tests/data/read_store_test_get_reads.in | 10 +
.../data/read_store_test_get_reads.reads_1.fq | 12 +
.../data/read_store_test_get_reads.reads_2.fq | 12 +
ariba/tests/data/read_store_test_sort_file.in | 10 +
ariba/tests/data/read_store_test_sort_file.out | 10 +
.../data/ref_preparer_test_write_info_file.out | 5 +
...ence_data_filter_bad_data_metadata.expected.tsv | 9 +
.../reference_data_filter_bad_data_metadata.in.tsv | 20 +
...nce_data_filter_bad_data_non_coding.expected.fa | 2 +
...reference_data_filter_bad_data_non_coding.in.fa | 2 +
...ta_filter_bad_data_presence_absence.expected.fa | 6 +
...nce_data_filter_bad_data_presence_absence.in.fa | 6 +
..._data_filter_bad_data_variants_only.expected.fa | 2 +
...erence_data_filter_bad_data_variants_only.in.fa | 6 +
ariba/tests/data/reference_data_get_filename | 1 +
ariba/tests/data/reference_data_init.tsv | 4 +
.../data/reference_data_init_empty.fa} | 0
.../data/reference_data_init_presence_absence.fa | 4 +
.../data/reference_data_keep_seqs_from_dict.fa | 2 +
.../data/reference_data_keep_seqs_from_dict.log | 1 +
ariba/tests/data/reference_data_load_fasta_file.fa | 2 +
.../data/reference_data_load_metadata_tsv.tsv | 3 +
.../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 | 10 +
.../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 | 11 +
.../reference_data_sequence.presence_absence.fa | 2 +
...erence_data_sequence_length.presence_absence.fa | 2 +
.../data/reference_data_sequence_type.noncoding.fa | 2 +
...eference_data_sequence_type.presence_absence.fa | 2 +
.../reference_data_sequence_type.variants_only.fa | 2 +
...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 | 12 +
...rence_data_test_cluster_with_cdhit.clusters.tsv | 3 +
..._cluster_with_cdhit.expected_representatives.fa | 10 +
...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 +
...it_clusters_in_file.expected_representatives.fa | 16 +
...uster_with_cdhit_clusters_in_file.non_coding.fa | 10 +
...with_cdhit_clusters_in_file.presence_absence.fa | 10 +
..._test_cluster_with_cdhit_nocluster.clusters.tsv | 6 +
...ith_cdhit_nocluster.expected_representatives.fa | 20 +
...test_cluster_with_cdhit_nocluster.non_coding.fa | 10 +
...luster_with_cdhit_nocluster.presence_absence.fa | 10 +
.../data/reference_data_test_remove_bad_genes.log | 5 +
.../data/reference_data_test_rename_sequences.out | 8 +
...ata_test_write_cluster_allocation_file.expected | 4 +
...rence_data_test_write_seqs_to_fasta.expected.fa | 6 +
.../reference_data_test_write_seqs_to_fasta.in.fa | 10 +
...a => reference_data_write_dict_of_sequences.fa} | 6 +-
.../reference_data_write_metadata_tsv.expected.tsv | 2 +
.../data/reference_data_write_metadata_tsv.tsv | 2 +
...nce_data_write_metadata_tsv_presence_absence.fa | 4 +
ariba/tests/data/report_filter_test_init_bad.tsv | 4 +
ariba/tests/data/report_filter_test_init_good.tsv | 5 +
.../data/report_filter_test_load_report_bad.tsv | 4 +
.../data/report_filter_test_load_report_good.tsv | 5 +
.../tests/data/report_filter_test_run.expected.tsv | 6 +
ariba/tests/data/report_filter_test_run.in.tsv | 9 +
.../tests/data/report_filter_test_write_report.tsv | 4 +
...mtools_variants_test_get_depths_at_position.bam | Bin 0 -> 4744 bytes
...ols_variants_test_get_depths_at_position.ref.fa | 18 +
...variants_test_get_depths_at_position.ref.fa.fai | 1 +
...z => samtools_variants_test_get_read_depths.gz} | Bin
... samtools_variants_test_get_read_depths.gz.tbi} | Bin
...riants_test_get_variant_positions_from_vcf.vcf} | 0
...ools_variants_test_get_variants.read_depths.gz} | Bin
..._variants_test_get_variants.read_depths.gz.tbi} | Bin
...vcf => samtools_variants_test_get_variants.vcf} | 0
...est_make_vcf_and_read_depths_files.assembly.fa} | 0
...make_vcf_and_read_depths_files.assembly.fa.fai} | 0
...riants_test_make_vcf_and_read_depths_files.bam} | Bin
..._and_read_depths_files.expected.read_depths.gz} | Bin
..._read_depths_files.expected.read_depths.gz.tbi} | Bin
...st_make_vcf_and_read_depths_files.expected.vcf} | 0
.../samtools_variants_test_total_depth_per_contig | 7 +
... samtools_variants_test_variants_in_coords.vcf} | 0
.../summary_sample_test_column_names_tuples.tsv | 8 +
.../summary_sample_test_column_summary_data.tsv | 8 +
.../data/summary_sample_test_load_file.in.tsv | 7 +
.../summary_sample_test_non_synon_variants.tsv | 8 +
.../tests/data/summary_sample_test_var_groups.tsv | 7 +
.../data/summary_test_gather_output_rows.in.1.tsv | 7 +-
.../data/summary_test_gather_output_rows.in.2.tsv | 8 +-
.../data/summary_test_get_all_cluster_names.1.tsv | 3 +
.../data/summary_test_get_all_cluster_names.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_test_load_file.in.tsv | 5 -
.../tests/data/summary_test_load_input_files.1.tsv | 3 +
.../tests/data/summary_test_load_input_files.2.tsv | 5 +
.../summary_test_newick_from_dist_matrix.distances | 4 +
.../data/summary_test_newick_from_dist_matrix.tre | 1 +
.../summary_test_write_distance_matrix.distances | 4 +
ariba/tests/data/summary_test_write_tsv.out.tsv | 3 -
ariba/tests/data/test_common_cat_files.in.1 | 2 +
ariba/tests/data/test_common_cat_files.in.2 | 3 +
ariba/tests/data/test_common_cat_files.in.3 | 1 +
ariba/tests/data/test_common_cat_files.out | 6 +
ariba/tests/data/vfdb_parser_test_run.in.fa | 6 +
ariba/tests/data/vfdb_parser_test_run.out.fa | 6 +
ariba/tests/data/vfdb_parser_test_run.out.tsv | 2 +
ariba/tests/external_progs_test.py | 9 +
ariba/tests/faidx_test.py | 5 +-
ariba/tests/flag_test.py | 11 +-
ariba/tests/mapping_test.py | 134 +-
ariba/tests/read_store_test.py | 80 ++
ariba/tests/ref_preparer_test.py | 121 ++
ariba/tests/refcheck_test.py | 69 -
ariba/tests/reference_data_test.py | 678 ++++++++++
ariba/tests/report_filter_test.py | 335 +++++
ariba/tests/samtools_variants_test.py | 173 +++
ariba/tests/sequence_metadata_test.py | 89 ++
ariba/tests/sequence_variant_test.py | 100 ++
ariba/tests/summary_cluster_test.py | 424 +++++++
ariba/tests/summary_sample_test.py | 104 ++
ariba/tests/summary_test.py | 503 ++++++--
ariba/tests/versions_test.py | 8 +
ariba/tests/vfdb_parser_test.py | 60 +
ariba/versions.py | 66 +
ariba/vfdb_parser.py | 46 +
install_dependencies.sh | 115 ++
scripts/ariba | 14 +-
setup.py | 11 +-
374 files changed, 14344 insertions(+), 3389 deletions(-)
create mode 100644 .travis.yml
create mode 100644 ariba/aln_to_metadata.py
create mode 100644 ariba/assembly.py
create mode 100644 ariba/assembly_compare.py
create mode 100644 ariba/assembly_variants.py
create mode 100644 ariba/best_seq_chooser.py
create mode 100644 ariba/card_record.py
create mode 100644 ariba/read_store.py
create mode 100644 ariba/ref_genes_getter.py
create mode 100644 ariba/ref_preparer.py
delete mode 100644 ariba/refcheck.py
create mode 100644 ariba/reference_data.py
create mode 100644 ariba/report.py
create mode 100644 ariba/report_filter.py
create mode 100644 ariba/samtools_variants.py
create mode 100644 ariba/sequence_metadata.py
create mode 100644 ariba/sequence_variant.py
create mode 100644 ariba/summary_cluster.py
create mode 100644 ariba/summary_sample.py
create mode 100644 ariba/tasks/aln2meta.py
create mode 100644 ariba/tasks/getref.py
create mode 100644 ariba/tasks/prepareref.py
delete mode 100644 ariba/tasks/refcheck.py
create mode 100644 ariba/tasks/reportfilter.py
create mode 100644 ariba/tasks/test.py
create mode 100644 ariba/test_run_data/metadata.tsv
create mode 100644 ariba/test_run_data/non_coding.fa
create mode 100644 ariba/test_run_data/presence_absence.fa
create mode 100644 ariba/test_run_data/reads_1.fq
create mode 100644 ariba/test_run_data/reads_2.fq
create mode 100644 ariba/test_run_data/ref_fasta_to_make_reads_from.fa
create mode 100644 ariba/test_run_data/variants_only.fa
create mode 100644 ariba/tests/aln_to_metadata_test.py
create mode 100644 ariba/tests/assembly_compare_test.py
create mode 100644 ariba/tests/assembly_test.py
create mode 100644 ariba/tests/assembly_variants_test.py
create mode 100644 ariba/tests/best_seq_chooser_test.py
create mode 100644 ariba/tests/card_record_test.py
create mode 100644 ariba/tests/common_test.py
create mode 100644 ariba/tests/data/aln_to_metadata_load_aln_file.in.fa
create mode 100644 ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_make_cluster_file.out
create mode 100644 ariba/tests/data/aln_to_metadata_run_coding.in.fa
create mode 100644 ariba/tests/data/aln_to_metadata_run_coding.in.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_run_coding.out.cluster
create mode 100644 ariba/tests/data/aln_to_metadata_run_coding.out.fa
create mode 100644 ariba/tests/data/aln_to_metadata_run_coding.out.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_run_noncoding.in.fa
create mode 100644 ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv
create mode 100644 ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster
create mode 100644 ariba/tests/data/aln_to_metadata_run_noncoding.out.fa
create mode 100644 ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv
create mode 100644 ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords
rename ariba/tests/data/{cluster_test_assemble_with_spades/reads_1.fq => assembly_test_assemble_with_spades_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_assemble_with_spades/reads_2.fq => assembly_test_assemble_with_spades_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_assemble_with_spades.gene.fa => assembly_test_assemble_with_spades_ref.fa} (100%)
create mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.bad
create mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.good
rename ariba/tests/data/{cluster_test_fix_contig_orientation.in.fa => assembly_test_fix_contig_orientation.in.fa} (77%)
rename ariba/tests/data/{cluster_test_fix_contig_orientation.out.fa => assembly_test_fix_contig_orientation.out.fa} (77%)
rename ariba/tests/data/{cluster_test_fix_contig_orientation.gene.fa => assembly_test_fix_contig_orientation.ref.fa} (100%)
rename ariba/tests/data/{cluster_test_gapfill_with_gapfiller.scaffolds_no_gaps.fa => assembly_test_gapfill_with_gapfiller.scaffolds_no_gaps.fa} (100%)
rename ariba/tests/data/{cluster_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa => assembly_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa} (100%)
rename ariba/tests/data/{cluster_test_gapfill_with_gapfiller/reads_1.fq => assembly_test_gapfill_with_gapfiller_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_gapfill_with_gapfiller/reads_2.fq => assembly_test_gapfill_with_gapfiller_reads_2.fq} (100%)
create mode 100644 ariba/tests/data/assembly_test_has_gaps_to_fill.has_gaps.fa
create mode 100644 ariba/tests/data/assembly_test_has_gaps_to_fill.no_gaps.fa
rename ariba/tests/data/{cluster_test_parse_assembly_bam.assembly.fa => assembly_test_parse_assembly_bam.assembly.fa} (100%)
rename ariba/tests/data/{cluster_test_parse_assembly_bam.bam => assembly_test_parse_assembly_bam.bam} (100%)
rename ariba/tests/data/{cluster_test_rename_scaffolds.in.fa => assembly_test_rename_scaffolds.in.fa} (100%)
create mode 100644 ariba/tests/data/assembly_test_rename_scaffolds.out.fa
rename ariba/tests/data/{cluster_test_scaffold_with_sspace.contigs.fa => assembly_test_scaffold_with_sspace_contigs.fa} (100%)
rename ariba/tests/data/{cluster_test_scaffold_with_sspace/reads_1.fq => assembly_test_scaffold_with_sspace_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_scaffold_with_sspace/reads_2.fq => assembly_test_scaffold_with_sspace_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_fix_contig_orientation/reads_1.fq => assembly_test_set_assembly_kmer_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_fix_contig_orientation/reads_2.fq => assembly_test_set_assembly_kmer_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_get_mummer_variants.none.snps => assembly_variants_test_get_mummer_variants.none.snps} (100%)
rename ariba/tests/data/{cluster_test_get_mummer_variants.snp.snps => assembly_variants_test_get_mummer_variants.snp.snps} (100%)
create mode 100644 ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_metadata.tsv
create mode 100644 ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_coding_presence_absence.fa
create mode 100644 ariba/tests/data/assembly_variants_test_get_one_variant_for_one_contig_non_coding.metadata.tsv
create mode 100644 ariba/tests/data/assembly_variants_test_get_variants_non_coding.fa
create mode 100644 ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa
create mode 100644 ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
create mode 100644 ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa
create mode 100644 ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
rename ariba/tests/data/{cluster_test_choose_best_gene/reads_1.fq => best_seq_chooser_best_seq_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_choose_best_gene/reads_2.fq => best_seq_chooser_best_seq_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_choose_best_gene/genes.fa => best_seq_chooser_best_seq_ref.fa} (100%)
create mode 100644 ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai
rename ariba/tests/data/{cluster_test_get_best_gene_by_alignment_score/reads_1.fq => best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_get_best_gene_by_alignment_score/reads_2.fq => best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_get_best_gene_by_alignment_score/genes.fa => best_seq_chooser_get_best_seq_by_alignment_score_ref.fa} (100%)
create mode 100644 ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai
rename ariba/tests/data/{cluster_test_get_total_alignment_score/reads_1.fq => best_seq_chooser_total_alignment_score_reads_1.fq} (100%)
rename ariba/tests/data/{cluster_test_get_total_alignment_score/reads_2.fq => best_seq_chooser_total_alignment_score_reads_2.fq} (100%)
rename ariba/tests/data/{cluster_test_get_total_alignment_score/genes.fa => best_seq_chooser_total_alignment_score_ref_seqs.fa} (100%)
create mode 100644 ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai
delete mode 100644 ariba/tests/data/cdhit_test_enumerate_fasta.in.fa
delete mode 100644 ariba/tests/data/cdhit_test_enumerate_fasta.out.fa
create mode 100644 ariba/tests/data/cdhit_test_load_user_clusters_file.bad1
create mode 100644 ariba/tests/data/cdhit_test_load_user_clusters_file.bad2
create mode 100644 ariba/tests/data/cdhit_test_load_user_clusters_file.bad3
create mode 100644 ariba/tests/data/cdhit_test_load_user_clusters_file.good
delete mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.in.fa
delete mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.in.renamed.fa
create mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.infile
delete mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa
delete mode 100644 ariba/tests/data/cdhit_test_parse_cluster_info_file.out.fa.bak.clstr
create mode 100644 ariba/tests/data/cdhit_test_rename_clusters.expected.fa
create mode 100644 ariba/tests/data/cdhit_test_rename_clusters.in.fa
delete mode 100644 ariba/tests/data/cdhit_test_rename_fasta.in.fa
create mode 100644 ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters
copy ariba/tests/data/{cdhit_test_rename_fasta.out.fa => cdhit_test_run_get_clusters_from_dict.in.fa} (54%)
create mode 100644 ariba/tests/data/cdhit_test_run_get_clusters_from_dict.out.fa
delete mode 100644 ariba/tests/data/cluster_test_assemble_with_spades/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_choose_best_gene.gene.fa
create mode 100644 ariba/tests/data/cluster_test_count_reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_count_reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_fix_contig_orientation/genes.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_assembly_fail.noncoding.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_choose_ref_fail.presence_absence.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_non_coding.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.always_report.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa
delete mode 100644 ariba/tests/data/cluster_test_gapfill_with_gapfiller.gene.fa
delete mode 100644 ariba/tests/data/cluster_test_gapfill_with_gapfiller/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_generic/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_generic/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_generic/reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts/reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts_fail/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts_fail/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_get_read_counts_fail/reads_2.fq
rename ariba/tests/data/{cluster_test_init_no_gene_fa => cluster_test_init_no_refs_fa}/reads_1.fq (100%)
rename ariba/tests/data/{cluster_test_init_no_gene_fa => cluster_test_init_no_refs_fa}/reads_2.fq (100%)
create mode 100644 ariba/tests/data/cluster_test_init_refdata.fa
delete mode 100644 ariba/tests/data/cluster_test_load_final_contigs.contigs.fa
delete mode 100644 ariba/tests/data/cluster_test_load_final_contigs/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_load_final_contigs/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_load_final_contigs/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq
create mode 100644 ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq
create mode 100644 ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq
create mode 100644 ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq
delete mode 100644 ariba/tests/data/cluster_test_make_report_lines.read_depths.gz
delete mode 100644 ariba/tests/data/cluster_test_make_report_lines.read_depths.gz.tbi
delete mode 100644 ariba/tests/data/cluster_test_nucmer_hits_to_assembled_gene_sequences.expected.out.fa
create mode 100644 ariba/tests/data/cluster_test_number_of_reads_for_assembly.ref.fa
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_bam/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_bam/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_bam/reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords.coords
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_parse_assembly_vs_gene_coords/reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds.out.fa
delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds/reads_2.fq
delete mode 100644 ariba/tests/data/cluster_test_scaffold_with_sspace.gene.fa
delete mode 100644 ariba/tests/data/cluster_test_scaffold_with_sspace/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_set_assembly_kmer/genes.fa
delete mode 100644 ariba/tests/data/cluster_test_set_assembly_kmer/reads_1.fq
delete mode 100644 ariba/tests/data/cluster_test_set_assembly_kmer/reads_2.fq
delete mode 100644 ariba/tests/data/clusters_test_bam_to_clusters.out.ref2.reads_1.fq
delete mode 100644 ariba/tests/data/clusters_test_bam_to_clusters.out.ref2.reads_2.fq
create mode 100644 ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai
create mode 100644 ariba/tests/data/clusters_test_bam_to_clusters_reads.read_store.gz
create mode 100644 ariba/tests/data/clusters_test_bam_to_clusters_reads_no_reads_map.bam
rename ariba/tests/data/{clusters_test_bam_to_clusters.out.ref1.reads_1.fq => clusters_test_bam_to_clusters_reads_no_reads_map_1.fq} (54%)
rename ariba/tests/data/{clusters_test_bam_to_clusters.out.ref1.reads_2.fq => clusters_test_bam_to_clusters_reads_no_reads_map_2.fq} (54%)
create mode 100644 ariba/tests/data/clusters_test_load_data_info_file
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/cdhit.clusters.pickle
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/info.txt
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/refcheck.01.check_variants.non_coding.fa
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/refcheck.01.check_variants.presence_absence.fa
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/refcheck.01.check_variants.tsv
create mode 100644 ariba/tests/data/clusters_test_load_reference_data_from_dir/refcheck.01.check_variants.variants_only.fa
delete mode 100644 ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.in.gene1.fa
delete mode 100644 ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.in.gene2.fa
create mode 100644 ariba/tests/data/clusters_test_write_catted_genes_matching_refs_fasta.expected.out.fa
create mode 100644 ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam
create mode 100644 ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq
create mode 100644 ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq
rename ariba/tests/data/{clusters_test_sam_pair_to_insert.bam => mapping_test_sam_pair_to_insert.bam} (100%)
rename ariba/tests/data/{clusters_test_sam_to_fastq.bam => mapping_test_sam_to_fastq.bam} (100%)
delete mode 100644 ariba/tests/data/mapping_test_smalt_reads_1.fq
delete mode 100644 ariba/tests/data/mapping_test_smalt_reads_2.fq
delete mode 100644 ariba/tests/data/mapping_test_smalt_ref.fa
delete mode 100644 ariba/tests/data/mapping_test_smalt_ref.fa.fai
delete mode 100644 ariba/tests/data/mapping_test_smalt_sorted.bam
delete mode 100644 ariba/tests/data/mapping_test_smalt_unsorted.bam
create mode 100644 ariba/tests/data/read_store_test_clean.in
create mode 100644 ariba/tests/data/read_store_test_compress_and_index_file.in
create mode 100644 ariba/tests/data/read_store_test_get_reads.in
create mode 100644 ariba/tests/data/read_store_test_get_reads.reads_1.fq
create mode 100644 ariba/tests/data/read_store_test_get_reads.reads_2.fq
create mode 100644 ariba/tests/data/read_store_test_sort_file.in
create mode 100644 ariba/tests/data/read_store_test_sort_file.out
create mode 100644 ariba/tests/data/ref_preparer_test_write_info_file.out
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_metadata.expected.tsv
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_non_coding.expected.fa
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_presence_absence.expected.fa
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_variants_only.expected.fa
create mode 100644 ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa
create mode 100644 ariba/tests/data/reference_data_get_filename
create mode 100644 ariba/tests/data/reference_data_init.tsv
copy ariba/{tasks/__init__.py => tests/data/reference_data_init_empty.fa} (100%)
create mode 100644 ariba/tests/data/reference_data_init_presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_keep_seqs_from_dict.fa
create mode 100644 ariba/tests/data/reference_data_keep_seqs_from_dict.log
create mode 100644 ariba/tests/data/reference_data_load_fasta_file.fa
create mode 100644 ariba/tests/data/reference_data_load_metadata_tsv.tsv
create mode 100644 ariba/tests/data/reference_data_make_catted_fasta.expected.fa
create mode 100644 ariba/tests/data/reference_data_make_catted_fasta.noncoding.fa
create mode 100644 ariba/tests/data/reference_data_make_catted_fasta.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_make_catted_fasta.variants_only.fa
create mode 100644 ariba/tests/data/reference_data_remove_bad_genes.in.fa
create mode 100644 ariba/tests/data/reference_data_rename_sequences.noncoding.fa
create mode 100644 ariba/tests/data/reference_data_rename_sequences.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_rename_sequences.variants_only.fa
create mode 100644 ariba/tests/data/reference_data_rename_sequences_metadata.tsv
create mode 100644 ariba/tests/data/reference_data_sequence.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_sequence_length.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_sequence_type.noncoding.fa
create mode 100644 ariba/tests/data/reference_data_sequence_type.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_sequence_type.variants_only.fa
create mode 100644 ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.noncoding.fa
create mode 100644 ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.pres_abs.fa
create mode 100644 ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.var_only.fa
create mode 100644 ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit.clusters.tsv
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit.expected_representatives.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit.non_coding.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.clusters
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.clusters.tsv
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.expected_representatives.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.non_coding.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_clusters_in_file.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.clusters.tsv
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.expected_representatives.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.non_coding.fa
create mode 100644 ariba/tests/data/reference_data_test_cluster_with_cdhit_nocluster.presence_absence.fa
create mode 100644 ariba/tests/data/reference_data_test_remove_bad_genes.log
create mode 100644 ariba/tests/data/reference_data_test_rename_sequences.out
create mode 100644 ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected
create mode 100644 ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa
create mode 100644 ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa
rename ariba/tests/data/{cdhit_test_rename_fasta.out.fa => reference_data_write_dict_of_sequences.fa} (50%)
create mode 100644 ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv
create mode 100644 ariba/tests/data/reference_data_write_metadata_tsv.tsv
create mode 100644 ariba/tests/data/reference_data_write_metadata_tsv_presence_absence.fa
create mode 100644 ariba/tests/data/report_filter_test_init_bad.tsv
create mode 100644 ariba/tests/data/report_filter_test_init_good.tsv
create mode 100644 ariba/tests/data/report_filter_test_load_report_bad.tsv
create mode 100644 ariba/tests/data/report_filter_test_load_report_good.tsv
create mode 100644 ariba/tests/data/report_filter_test_run.expected.tsv
create mode 100644 ariba/tests/data/report_filter_test_run.in.tsv
create mode 100644 ariba/tests/data/report_filter_test_write_report.tsv
create mode 100644 ariba/tests/data/samtools_variants_test_get_depths_at_position.bam
create mode 100644 ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa
create mode 100644 ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai
rename ariba/tests/data/{cluster_test_get_assembly_read_depths.gz => samtools_variants_test_get_read_depths.gz} (100%)
rename ariba/tests/data/{cluster_test_get_assembly_read_depths.gz.tbi => samtools_variants_test_get_read_depths.gz.tbi} (100%)
rename ariba/tests/data/{cluster_test_get_samtools_variant_positions.vcf => samtools_variants_test_get_variant_positions_from_vcf.vcf} (100%)
rename ariba/tests/data/{cluster_test_get_samtools_variants.read_depths.gz => samtools_variants_test_get_variants.read_depths.gz} (100%)
rename ariba/tests/data/{cluster_test_get_samtools_variants.read_depths.gz.tbi => samtools_variants_test_get_variants.read_depths.gz.tbi} (100%)
rename ariba/tests/data/{cluster_test_get_samtools_variants.vcf => samtools_variants_test_get_variants.vcf} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.fa => samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.fa.fai => samtools_variants_test_make_vcf_and_read_depths_files.assembly.fa.fai} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.bam => samtools_variants_test_make_vcf_and_read_depths_files.bam} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.read_depths.gz => samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.read_depths.gz.tbi => samtools_variants_test_make_vcf_and_read_depths_files.expected.read_depths.gz.tbi} (100%)
rename ariba/tests/data/{cluster_test_make_assembly_vcf.assembly.vcf => samtools_variants_test_make_vcf_and_read_depths_files.expected.vcf} (100%)
create mode 100644 ariba/tests/data/samtools_variants_test_total_depth_per_contig
rename ariba/tests/data/{cluster_test_get_vcf_variant_counts.vcf => samtools_variants_test_variants_in_coords.vcf} (100%)
create mode 100644 ariba/tests/data/summary_sample_test_column_names_tuples.tsv
create mode 100644 ariba/tests/data/summary_sample_test_column_summary_data.tsv
create mode 100644 ariba/tests/data/summary_sample_test_load_file.in.tsv
create mode 100644 ariba/tests/data/summary_sample_test_non_synon_variants.tsv
create mode 100644 ariba/tests/data/summary_sample_test_var_groups.tsv
create mode 100644 ariba/tests/data/summary_test_get_all_cluster_names.1.tsv
create mode 100644 ariba/tests/data/summary_test_get_all_cluster_names.2.tsv
create mode 100644 ariba/tests/data/summary_test_get_all_var_groups.1.tsv
create mode 100644 ariba/tests/data/summary_test_get_all_var_groups.2.tsv
delete mode 100644 ariba/tests/data/summary_test_load_file.in.tsv
create mode 100644 ariba/tests/data/summary_test_load_input_files.1.tsv
create mode 100644 ariba/tests/data/summary_test_load_input_files.2.tsv
create mode 100644 ariba/tests/data/summary_test_newick_from_dist_matrix.distances
create mode 100644 ariba/tests/data/summary_test_newick_from_dist_matrix.tre
create mode 100644 ariba/tests/data/summary_test_write_distance_matrix.distances
delete mode 100644 ariba/tests/data/summary_test_write_tsv.out.tsv
create mode 100644 ariba/tests/data/test_common_cat_files.in.1
create mode 100644 ariba/tests/data/test_common_cat_files.in.2
create mode 100644 ariba/tests/data/test_common_cat_files.in.3
create mode 100644 ariba/tests/data/test_common_cat_files.out
create mode 100644 ariba/tests/data/vfdb_parser_test_run.in.fa
create mode 100644 ariba/tests/data/vfdb_parser_test_run.out.fa
create mode 100644 ariba/tests/data/vfdb_parser_test_run.out.tsv
create mode 100644 ariba/tests/external_progs_test.py
create mode 100644 ariba/tests/read_store_test.py
create mode 100644 ariba/tests/ref_preparer_test.py
delete mode 100644 ariba/tests/refcheck_test.py
create mode 100644 ariba/tests/reference_data_test.py
create mode 100644 ariba/tests/report_filter_test.py
create mode 100644 ariba/tests/samtools_variants_test.py
create mode 100644 ariba/tests/sequence_metadata_test.py
create mode 100644 ariba/tests/sequence_variant_test.py
create mode 100644 ariba/tests/summary_cluster_test.py
create mode 100644 ariba/tests/summary_sample_test.py
create mode 100644 ariba/tests/versions_test.py
create mode 100644 ariba/tests/vfdb_parser_test.py
create mode 100644 ariba/versions.py
create mode 100644 ariba/vfdb_parser.py
create mode 100755 install_dependencies.sh
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git
More information about the debian-med-commit
mailing list