Mercurial > repos > iuc > qiime_pick_open_reference_otus
changeset 1:d68b2ef52012 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1
| author | iuc |
|---|---|
| date | Thu, 22 Jun 2017 07:00:25 -0400 |
| parents | f668a753bcfc |
| children | 845b4664b98a |
| files | generate_test_data.sh generate_test_data.sh.orig macros.xml test-data/assign_taxonomy/mothur_id_to_taxonomy.txt test-data/assign_taxonomy/mothur_repr_set_seqs.fasta test-data/assign_taxonomy/sortmerna_input_seqs.fasta test-data/assign_taxonomy/sortmerna_map.blast test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt test-data/assign_taxonomy/uclust_taxonomic_assignation.txt |
| diffstat | 9 files changed, 56 insertions(+), 388 deletions(-) [+] |
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--- a/generate_test_data.sh Fri May 19 03:55:46 2017 -0400 +++ b/generate_test_data.sh Thu Jun 22 07:00:25 2017 -0400 @@ -92,9 +92,32 @@ --similarity '0.9' \ --uclust_max_accepts '3' \ -o assign_taxonomy_uclust -cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt' +ls assign_taxonomy_uclust +md5sum 'assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt' rm -rf assign_taxonomy_uclust +assign_taxonomy.py \ + --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \ + --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ + --assignment_method 'mothur' \ + --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ + --confidence '0.5' \ + -o assign_taxonomy_mothur +ls assign_taxonomy_mothur +md5sum 'assign_taxonomy_mothur/mothur_repr_set_seqs_tax_assignments.txt' +rm -rf assign_taxonomy_mothur + +assign_taxonomy.py \ + --input_fasta_fp 'test-data/assign_taxonomy/mothur_repr_set_seqs.fasta' \ + --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ + --assignment_method 'mothur' \ + --reference_seqs_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ + --blast_e_value '0.001' \ + -o assign_taxonomy_blast +ls assign_taxonomy_blast +md5sum 'assign_taxonomy_blast/mothur_repr_set_seqs_tax_assignments.txt' +rm -rf assign_taxonomy_blast + #assign_taxonomy.py \ # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \ # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \ @@ -116,14 +139,6 @@ # -o assign_taxonomy_rtax #ls assign_taxonomy_rtax -#assign_taxonomy.py \ -# --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ -# --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ -# --assignment_method 'mothur' \ -# --confidence 0.5 \ -# -o assign_taxonomy_mothur -#ls assign_taxonomy_mothur - assign_taxonomy.py \ --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ --assignment_method 'sortmerna' \ @@ -133,8 +148,9 @@ --sortmerna_coverage "0.9" \ --sortmerna_best_N_alignments "5" \ -o assign_taxonomy_sortmerna -cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast' -cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt' +ls assign_taxonomy_sortmerna +md5sum 'assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt' +md5sum 'assign_taxonomy_sortmerna/sortmerna_map.blast' rm -rf assign_taxonomy_sortmerna #beta_diversity @@ -1105,22 +1121,3 @@ cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log' cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt' rm -rf validate_mapping_file_output - - - - - - - - - - - - - - - - - - -
--- a/generate_test_data.sh.orig Fri May 19 03:55:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,312 +0,0 @@ -#!/usr/bin/env bash - -# validate_mapping_file -validate_mapping_file.py \ - -m 'test-data/validate_mapping_file/map.tsv' \ - -o validate_mapping_file_output \ - -c '_' -cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html' -cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log' -cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt' -rm -rf validate_mapping_file_output - -# split_libraries_fastq -split_libraries_fastq.py \ - --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \ - -o split_libraries \ - --mapping_fps 'test-data/map.tsv' \ - --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \ - --store_qual_scores \ - --store_demultiplexed_fastq \ - --max_bad_run_length 3 \ - --min_per_read_length_fraction 0.75 \ - --sequence_max_n 0 \ - --start_seq_id 0 \ - --barcode_type 'golay_12' \ - --max_barcode_errors 1.5 -cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular' -cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta' -cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual' -cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq' -rm -rf split_libraries - -# split_libraries -split_libraries.py \ - --map 'test-data/split_libraries/mapping_file.txt' \ - -o split_libraries \ - --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \ - --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \ - --min_qual_score 25 \ - --qual_score_window 0 \ - --record_qual_scores \ - --min_seq_length 200 \ - --max_seq_length 1000 \ - --max_ambig 6 \ - --max_homopolymer 6 \ - --max_primer_mismatch 0 \ - --barcode_type 'golay_12' \ - --max_barcode_errors 1.5 \ - --start_numbering_at 1 -cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna' -cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log' -cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt' -cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual' -rm -rf split_libraries - -# pick_open_reference_otus -pick_open_reference_otus.py \ - --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ - -o pick_open_reference_otus_1 \ - --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ - --otu_picking_method 'uclust' \ - --new_ref_set_id 'New' \ - --parallel \ - --percent_subsample '0.001' \ - --prefilter_percent_id '0.0' \ - --minimum_failure_threshold '100000' \ - --min_otu_size '2' -cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt' -cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt' -cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre' -rm -rf pick_open_reference_otus_1 - -pick_open_reference_otus.py \ - --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ - -o pick_open_reference_otus_2 \ - --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ - --otu_picking_method 'uclust' \ - --new_ref_set_id 'New' \ - --parallel \ - --percent_subsample '0.001' \ - --prefilter_percent_id '0.0' \ - --minimum_failure_threshold '100000' \ - --min_otu_size '3' \ - --suppress_taxonomy_assignment \ - --suppress_align_and_tree -cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt' -cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt' -rm -rf pick_open_reference_otus_2 - -pick_open_reference_otus.py \ - --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \ - -o pick_open_reference_otus_3 \ - --reference_fp 'test-data/gg_13_8_79_otus.fasta' \ - --otu_picking_method 'uclust' \ - --new_ref_set_id 'New' \ - --parallel \ - --percent_subsample '0.001' \ - --prefilter_percent_id '0.0' \ - --minimum_failure_threshold '100000' \ - --min_otu_size '10' \ - --suppress_taxonomy_assignment -cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt' -cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt' -cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre' -rm -rf pick_open_reference_otus_3 - -# core_diversity_analyses -# Data are from test data in https://github.com/biocore/qiime -core_diversity_analyses.py \ - --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ - -o core_diversity_analyses_1 \ - --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ - --sampling_depth 22 \ - --tree_fp 'test-data/core_diversity_analyses/rep_set.tre' -cp core_diversity_analyses_1/bdiv_even22/unweighted_unifrac_pc.txt 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' -rm -rf core_diversity_analyses_1 - -core_diversity_analyses.py \ - --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \ - -o core_diversity_analyses_2 \ - --mapping_fp 'test-data/core_diversity_analyses/map.txt' \ - --sampling_depth 22 \ - --nonphylogenetic_diversity \ - --suppress_taxa_summary \ - --suppress_beta_diversity \ - --suppress_alpha_diversity \ - --suppress_group_significance -rm -rf core_diversity_analyses_2 - -# summarize_taxa -cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom' -cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt' - -summarize_taxa.py \ - -i 'test-data/summarize_taxa/otu_table.biom' \ - -o summarize_taxa_1 \ - -L '2,3,4,5,6' \ - -m 'test-data/summarize_taxa/map.txt' \ - --md_identifier "taxonomy" \ - --delimiter ";" -cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt" -cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt" -cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt" -cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt" -cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt" -rm -rf summarize_taxa_1 - -summarize_taxa.py \ - -i 'test-data/summarize_taxa/otu_table.biom' \ - -o summarize_taxa_2 \ - -L '3,6' \ - --md_identifier "taxonomy" \ - --delimiter ";" -cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt" -cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt" -rm -rf summarize_taxa_2 - -# make_emperor -cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt' -cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt' -cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt' - -make_emperor.py \ - --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ - -o make_emperor_1 \ - --map_fp 'test-data/make_emperor/map.txt' \ - --number_of_axes '10' \ - --add_unique_columns \ - --number_of_segments 8 -rm -rf make_emperor_1 - -make_emperor.py \ - --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \ - -o make_emperor_2 \ - --map_fp 'test-data/make_emperor/map.txt' \ - --number_of_axes '10' \ - --add_unique_columns \ - --number_of_segments 8 \ - --taxa_fp 'test-data/make_emperor/2_L3.txt' \ - --n_taxa_to_keep 10 -rm -rf make_emperor_2 - -#alpha_rarefaction -alpha_rarefaction.py \ - --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \ - --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \ - -o alpha_rarefaction \ - --num_steps '2' \ - --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \ - --min_rare_depth '10' \ - --max_rare_depth '50' \ - --retain_intermediate_files -rm -rf alpha_rarefaction - -##beta_diversity -beta_diversity.py \ - --input_path 'test-data/beta_diversity/otu_table.biom' \ - -o beta_diversity_1 \ - --metrics 'unweighted_unifrac,weighted_unifrac' \ - --tree_path 'test-data/beta_diversity/rep_set.tre' -md5 'beta_diversity_1/unweighted_unifrac_otu_table.txt' -md5 'beta_diversity_1/weighted_unifrac_otu_table.txt' -rm -rf beta_diversity_1 - -beta_diversity.py \ - --input_path 'test-data/beta_diversity/otu_table.biom' \ - -o beta_diversity_2 \ - --metrics 'abund_jaccard,binary_chisq,binary_chord,binary_euclidean,binary_hamming,binary_jaccard,binary_lennon,binary_ochiai,binary_pearson,binary_sorensen_dice,bray_curtis,canberra,chisq,chord,euclidean,gower,hellinger,kulczynski,manhattan,morisita_horn,pearson,soergel,spearman_approx,specprof,unifrac_g,unifrac_g_full_tree,unweighted_unifrac,unweighted_unifrac_full_tree,weighted_normalized_unifrac,weighted_unifrac' \ - --tree_path 'test-data/beta_diversity/rep_set.tre' -md5 'beta_diversity_2/canberra_otu_table.txt' -md5 'beta_diversity_2/pearson_otu_table.txt' -rm -rf beta_diversity_2 - -# jackknifed_beta_diversity -jackknifed_beta_diversity.py \ - --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \ - --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \ - -o jackknifed_beta_diversity \ - --seqs_per_sample '10' \ - --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \ - --master_tree 'consensus' \ - --parallel -rm -rf jackknifed_beta_diversity - -#beta_diversity_through_plots -beta_diversity_through_plots.py \ - --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \ - --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \ - --output_dir beta_diversity_through_plots \ - --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \ - --parallel -cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' -cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' -cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/' -cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/' -rm -rf beta_diversity_through_plots - -# assign_taxonomy -assign_taxonomy.py \ - --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \ - --assignment_method 'uclust' \ - --min_consensus_fraction '0.51' \ - --similarity '0.9' \ - --uclust_max_accepts '3' \ - -o assign_taxonomy_uclust -cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt' -rm -rf assign_taxonomy_uclust - -#assign_taxonomy.py \ -# --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \ -# --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \ -# --assignment_method 'rdp' \ -# --confidence '3' \ -# -o assign_taxonomy_rdp - -#assign_taxonomy.py \ -# --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \ -# --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \ -# --assignment_method 'rtax' \ -# --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \ -# --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \ -# --single_ok \ -# --no_single_ok_generic \ -# --read_id_regex "\S+\s+(\S+)" \ -# --amplicon_id_regex "(\S+)\s+(\S+?)\/" \ -# --header_id_regex "\S+\s+(\S+?)\/" \ -# -o assign_taxonomy_rtax -#ls assign_taxonomy_rtax - -#assign_taxonomy.py \ -# --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ -# --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \ -# --assignment_method 'mothur' \ -# --confidence 0.5 \ -# -o assign_taxonomy_mothur -#ls assign_taxonomy_mothur - -assign_taxonomy.py \ - --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \ - --assignment_method 'sortmerna' \ - --min_consensus_fraction "0.51" \ - --similarity "0.9" \ - --sortmerna_e_value "1.0" \ - --sortmerna_coverage "0.9" \ - --sortmerna_best_N_alignments "5" \ - -o assign_taxonomy_sortmerna -cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast' -cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt' -rm -rf assign_taxonomy_sortmerna -<<<<<<< HEAD -======= - -# filter_otus_from_otu_table -filter_otus_from_otu_table.py \ - --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ - --min_count '2' \ - --max_count '1000' \ - --min_samples '5' \ - --max_samples '350' \ - --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom' - -filter_otus_from_otu_table.py \ - --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ - --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ - --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom' - -filter_otus_from_otu_table.py \ - --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \ - --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \ - --negate_ids_to_exclude \ - --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom' ->>>>>>> Update of the Qiime_core generate_test_data script
--- a/macros.xml Fri May 19 03:55:46 2017 -0400 +++ b/macros.xml Thu Jun 22 07:00:25 2017 -0400 @@ -29,6 +29,22 @@ </when> </conditional> </xml> + <xml name="assign_taxonomy_reference_source"> + <conditional name="references"> + <param name="source_selector" type="select" label="Select a reference sequence file from"> + <option value="cached">The local cache</option> + <option value="history">The active history</option> + </param> + <when value="cached"> + <param argument="--reference_seqs_fp" label="Reference sequences either used to generate a blast database (Blast) or used as training sequences for the selected classifier (RDP, Mothur)" type="select"> + <options from_data_table="qiime_rep_set"/> + </param> + </when> + <when value="history"> + <param argument="--reference_seqs_fp" type="data" format="fasta" label="Reference sequences to search against"/> + </when> + </conditional> + </xml> <xml name="pick_otus_similarity"> <param argument="--similarity" type="float" value="0.97" label="Sequence similarity threshold"/> </xml>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assign_taxonomy/mothur_id_to_taxonomy.txt Thu Jun 22 07:00:25 2017 -0400 @@ -0,0 +1,7 @@ +X67228 Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Rhizobium +X73443 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Clostridium +AB004750 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter +xxxxxx Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas +AB004748 Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter +AB000278 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Photobacterium +AB000390 Bacteria;Proteobacteria;Gammaproteobacteria;Vibrionales;Vibrionaceae;Vibrio
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assign_taxonomy/mothur_repr_set_seqs.fasta Thu Jun 22 07:00:25 2017 -0400 @@ -0,0 +1,4 @@ +>X67228 some description +aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa +>EF503697 +TAAAATGACTAGCCTGCGAGTCACGCCGTAAGGCGTGGCATACAGGCTCAGTAACACGTAGTCAACATGCCCAAAGGACGTGGATAACCTCGGGAAACTGAGGATAAACCGCGATAGGCCAAGGTTTCTGGAATGAGCTATGGCCGAAATCTATATGGCCTTTGGATTGGACTGCGGCCGATCAGGCTGTTGGTGAGGTAATGGCCCACCAAACCTGTAACCGGTACGGGCTTTGAGAGAAGTAGCCCGGAGATGGGCACTGAGACAAGGGCCCAGGCCCTATGGGGCGCAGCAGGCGCGAAACCTCTGCAATAGGCGAAAGCCTGACAGGGTTACTCTGAGTGATGCCCGCTAAGGGTATCTTTTGGCACCTCTAAAAATGGTGCAGAATAAGGGGTGGGCAAGTCTGGTGTCAGCCGCCGCGGTAATACCAGCACCCCGAGTTGTCGGGACGATTATTGGGCCTAAAGCATCCGTAGCCTGTTCTGCAAGTCCTCCGTTAAATCCACCTGCTCAACGGATGGGCTGCGGAGGATACCGCAGAGCTAGGAGGCGGGAGAGGCAAACGGTACTCAGTGGGTAGGGGTAAAATCCATTGATCTACTGAAGACCACCAGTGGCGAAGGCGGTTTGCCAGAACGCGCTCGACGGTGAGGGATGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGGTAGTCCCAGCTGTAAACGGATGCAGACTCGGGTGATGGGGTTGGCTTCCGGCCCAACCCCAATTGCCCCCAGGCGAAGCCCGTTAAGATCTTGCCGCCCTGTCAGATGTCAGGGCCGCCAATACTCGAAACCTTAAAAGGAAATTGGGCGCGGGAAAAGTCACCAAAAGGGGGTTGAAACCCTGCGGGTTATATATTGTAAACC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assign_taxonomy/sortmerna_input_seqs.fasta Thu Jun 22 07:00:25 2017 -0400 @@ -0,0 +1,2 @@ +>X67228 +aacgaacgctggcggcaggcttaacacatgcaagtcgaacgctccgcaaggagagtggcagacgggtgagtaacgcgtgggaatctacccaaccctgcggaatagctctgggaaactggaattaataccgcatacgccctacgggggaaagatttatcggggatggatgagcccgcgttggattagctagttggtggggtaaaggcctaccaaggcgacgatccatagctggtctgagaggatgatcagccacattgggactgagacacggcccaaa
--- a/test-data/assign_taxonomy/sortmerna_map.blast Fri May 19 03:55:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -X67228 152350 98.6 277 4 0 1 277 22 298 5.76e-129 464 277M 100 -X67228 558499 97.1 275 8 0 1 275 2 276 1.05e-122 443 275M2S 99.3 -X67228 553706 97.5 277 7 0 1 277 1 277 4.7e-125 451 277M 100 -X67228 553981 95.7 277 12 0 1 277 2 278 1.55e-118 429 277M 100 -X67228 4423084 98.6 277 4 0 1 277 21 297 5.76e-129 464 277M 100 -X73443 179865 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5 -X73443 181718 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D20M1I26M1I115M1D54M 97.5 -X73443 193551 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5 -X73443 212341 96.3 269 2 8 8 276 2 268 2.31e-114 415 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5 -X73443 175883 96 269 3 8 8 276 2 268 4.66e-113 411 7S3M1I28M1I3M1I7M1D8M1D21M1I26M1I114M1D54M 97.5 -AB004750 3888577 100 339 0 0 1 339 26 364 1.61e-166 588 339M 100 -AB004750 581782 97.6 339 8 0 1 339 27 365 4.36e-156 554 339M 100 -AB004750 1108679 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100 -AB004750 1109844 97.9 339 7 0 1 339 26 364 2.16e-157 558 339M 100 -AB004750 4418165 99.7 339 1 0 1 339 28 366 3.25e-165 584 339M 100 -xxxxxx 1102995 97.5 361 8 1 1 361 22 383 2.94e-166 588 174M1D187M 100 -xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100 -xxxxxx 340031 95.6 361 13 3 1 361 23 386 1.07e-158 562 169M3D192M 100 -AB004748 581782 98 396 8 0 1 396 27 422 8.13e-186 653 396M 100 -AB004748 1108679 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100 -AB004748 1109844 98.2 396 7 0 1 396 26 421 4.04e-187 657 396M 100 -AB004748 3888577 100 396 0 0 1 396 26 421 3.01e-196 687 396M 100 -AB004748 561327 97.5 396 10 0 1 396 1 396 3.3e-183 644 396M 100 -AB000278 554346 98.6 368 5 0 1 368 6 373 4e-175 617 368M 100 -AB000278 160928 97 368 7 4 1 368 33 400 2.94e-166 588 33M1D5M1I8M1I2M1D318M 100 -AB000390 4433053 98.1 317 6 0 1 317 13 329 3.2e-147 524 317M 100 -AB000390 19456 94.4 317 14 4 1 317 12 328 4.28e-132 474 77M2D4M2I234M 100 -AB000390 4432126 94.4 317 14 4 1 317 13 329 4.28e-132 474 77M2D4M2I234M 100
--- a/test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt Fri May 19 03:55:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -#OTU ID taxonomy confidence num hits -AB004750 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5 -AB000390 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae 1.00 3 -xxxxxx k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Alteromonadales; f__Alteromonadaceae; g__Marinobacter; s__ 1.00 3 -X67228 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Rhizobiaceae 0.60 5 -AB000278 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae; g__Photobacterium 1.00 2 -AB004748 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__; s__ 0.60 5 -X73443 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae 1.00 5
--- a/test-data/assign_taxonomy/uclust_taxonomic_assignation.txt Fri May 19 03:55:46 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -11469739 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3 -11480235 k__Bacteria; p__OD1; c__; o__; f__; g__; s__ 1.00 1 -11460543 k__Bacteria; p__OP9; c__JS1; o__SB-45; f__; g__; s__ 1.00 3 -11460523 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfobacterales; f__Desulfobulbaceae; g__; s__ 1.00 3 -11472286 k__Bacteria; p__WS5; c__; o__; f__; g__; s__ 1.00 1 -11458037 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptococcaceae; g__Desulfosporosinus; s__meridiei 1.00 3 -11472384 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 0.67 3 -11469752 k__Bacteria; p__TM7; c__TM7-1; o__; f__; g__; s__ 1.00 3 -11480408 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 1.00 3 -11468680 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Burkholderia; s__ 1.00 3