[med-svn] [ariba] branch master updated (3faa354 -> 0776079)
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 14:13:02 UTC 2016
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sascha-guest pushed a change to branch master
in repository ariba.
from 3faa354 adjust deps
new 68e7acf bump version to 1.0.0
new 194d86c Imported Upstream version 1.0.0
new 37d3682 Merge tag 'upstream/1.0.0'
new ddaa4b4 drop patches for old version
new 0776079 get packaging up to date with new version
The 5 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 | 226 ++--
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 +
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...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
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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 +
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...ence_data_make_catted_fasta.presence_absence.fa | 2 +
...ference_data_make_catted_fasta.variants_only.fa | 2 +
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.../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 +
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...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 +
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...rence_data_test_write_seqs_to_fasta.expected.fa | 6 +
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...a => reference_data_write_dict_of_sequences.fa} | 6 +-
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ariba/tests/data/report_filter_test_init_bad.tsv | 4 +
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ariba/tests/data/report_filter_test_run.in.tsv | 9 +
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...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 +
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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 +
debian/changelog | 4 +-
debian/control | 5 +-
debian/patches/fix-spades-call.patch | 20 +
debian/patches/make_velvet_default | 12 -
debian/patches/relax-pysam-version.patch | 15 +
debian/patches/rename-cdhit.patch | 36 +
debian/patches/rename_cdhit_binary | 41 -
debian/patches/series | 7 +-
debian/patches/skip_unavailable_tests | 30 -
debian/patches/spelling | 12 -
debian/rules | 5 +-
install_dependencies.sh | 115 ++
scripts/ariba | 14 +-
setup.py | 9 +-
385 files changed, 14426 insertions(+), 3494 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
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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
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delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds.out.fa
delete mode 100644 ariba/tests/data/cluster_test_rename_scaffolds/genes.fa
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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%)
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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
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delete mode 100644 ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.in.gene1.fa
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create mode 100644 ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam
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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%)
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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
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create mode 100644 ariba/tests/data/reference_data_rename_sequences.noncoding.fa
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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
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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
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create mode 100644 ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa
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create mode 100644 ariba/tests/data/report_filter_test_write_report.tsv
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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%)
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