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(-) [+]
line wrap: on
line diff
--- 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
-
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--- 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