Mercurial > repos > iuc > pick_closed_reference_otus
diff generate_test_data.sh @ 0:768fb40ad1e8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author | iuc |
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date | Thu, 18 May 2017 09:37:50 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Thu May 18 09:37:50 2017 -0400 @@ -0,0 +1,1126 @@ +#!/usr/bin/env bash + +# Data are from test data in https://github.com/biocore/qiime + +# align_seqs +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_pynast_uclust' \ + --alignment_method 'pynast' \ + --pairwise_alignment_method 'uclust' \ + --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \ + --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_pynast_muscle' \ + --alignment_method 'pynast' \ + --pairwise_alignment_method 'muscle' \ + --min_length '50' \ + --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_pynast_pair_hmm' \ + --alignment_method 'pynast' \ + --pairwise_alignment_method 'pair_hmm' \ + --min_percent_id '0.75' + +#align_seqs.py \ +# --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ +# -o 'align_seqs_pynast_clustal' \ +# --alignment_method 'pynast' \ +# --pairwise_alignment_method 'clustal' \ +# --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_pynast_blast' \ + --alignment_method 'pynast' \ + --pairwise_alignment_method 'blast' \ + --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_pynast_mafft' \ + --alignment_method 'pynast' \ + --pairwise_alignment_method 'mafft' \ + --min_percent_id '0.75' + +#align_seqs.py \ +# --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ +# -o 'align_seqs_infernal' \ +# --alignment_method 'infernal' \ +# --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \ +# --min_percent_id '0.75' + +#align_seqs.py \ +# --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ +# -o 'align_seqs_clustalw' \ +# --alignment_method 'clustalw' \ +# --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_muscle' \ + --alignment_method 'muscle' \ + --min_percent_id '0.75' + +align_seqs.py \ + --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \ + -o 'align_seqs_mafft' \ + --alignment_method 'mafft' \ + --min_percent_id '0.75' + +#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 + +# 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 + +#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 + +#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 + +# compare_categories +compare_categories.py \ + --method 'adonis' \ + --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ + --mapping_file 'test-data/compare_categories/map.txt' \ + --categories 'Treatment' \ + -o compare_categories_1 \ + --num_permutations '999' +cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt" +rm -rf compare_categories_1 + +compare_categories.py \ + --method 'dbrda' \ + --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \ + --mapping_file 'test-data/compare_categories/map.txt' \ + --categories 'Treatment' \ + -o compare_categories_2 \ + --num_permutations '99' +cp compare_categories_2/* "test-data/compare_categories/" +rm -rf compare_categories_2 + +# core_diversity_analyses +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 + +# filter_alignment +filter_alignment.py \ + --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ + -o 'filter_alignment_default' \ + --allowed_gap_frac '0.999999' \ + --threshold '3.0' + +filter_alignment.py \ + --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ + -o 'filter_alignment_without_mask_filter_and_outliers' \ + --suppress_lane_mask_filter \ + --allowed_gap_frac '0.999999' \ + --remove_outliers \ + --threshold '3.0' + +filter_alignment.py \ + --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \ + -o 'filter_alignment_entropy' \ + --allowed_gap_frac '0.999999' \ + --threshold '3.0' \ + --entropy_threshold '0.1' + +# filter_fasta +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_otu_map.fasta' \ + --otu_map 'test-data/filter_fasta/otu_map.txt' + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \ + --otu_map 'test-data/filter_fasta/otu_map.txt' \ + --negate + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_seq_id.fasta' \ + --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt' + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_otu_table.fasta' \ + --biom_fp 'test-data/filter_fasta/otu_table.biom' + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \ + --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta' + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \ + --seq_id_prefix 'S5' + +filter_fasta.py \ + --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \ + --output_fasta_fp 'filter_fasta_sample_id.fasta' \ + --sample_id_fp 'test-data/filter_fasta/map.txt' + +# 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' + +# filter_samples_from_otu_table +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --min_count '150' +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --min_count '0' \ + --max_count '149' +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ + --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \ + -s 'Treatment:Control' +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \ + -s 'Treatment:*,!Control' +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +filter_samples_from_otu_table.py \ + --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \ + --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \ + --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \ + --negate_sample_id_fp +biom convert \ + -i 'test-data/filter_samples_from_otu_table/tmp.biom' \ + -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \ + --to-json +rm 'test-data/filter_samples_from_otu_table/tmp.biom' + +# filter_taxa_from_otu_table +filter_taxa_from_otu_table.py \ + --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ + --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \ + --metadata_field 'taxonomy' +biom convert \ + -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \ + --to-json +rm 'test-data/filter_taxa_from_otu_table/tmp.biom' + +filter_taxa_from_otu_table.py \ + --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ + --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \ + --metadata_field 'taxonomy' +biom convert \ + -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \ + --to-json +rm 'test-data/filter_taxa_from_otu_table/tmp.biom' + +filter_taxa_from_otu_table.py \ + --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \ + --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + --positive_taxa 'p__Firmicutes' \ + --negative_taxa 'c__Clostridia' \ + --metadata_field 'taxonomy' +biom convert \ + -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \ + -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \ + --to-json +rm 'test-data/filter_taxa_from_otu_table/tmp.biom' + +# 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 + +# 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 + +# make_otu_heatmap +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --imagetype 'pdf' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf' + +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --imagetype 'png' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png' + +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --imagetype 'svg' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg' + +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ + --imagetype 'pdf' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf' + +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ + --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \ + --imagetype 'pdf' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf' + +make_otu_heatmap.py \ + --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \ + --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \ + --category "Treatment" \ + --imagetype 'pdf' \ + --color_scheme "YlGn" \ + --width "5" \ + --height "5" \ + --dpi "200" \ + --obs_md_category "taxonomy" \ + --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf' + +# make_phylogeny +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \ + --tree_method 'fasttree' \ + --log_fp 'fasttree_tree_method_default.txt' \ + --root_method 'tree_method_default' + +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'raxml_v730.tre' \ + --tree_method 'raxml_v730' \ + --log_fp 'raxml_v730.txt' \ + --root_method 'tree_method_default' + +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'test-data/make_phylogeny/muscle.tre' \ + --tree_method 'muscle' \ + --log_fp 'muscle.txt' \ + --root_method 'tree_method_default' + +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'test-data/make_phylogeny/clustalw.tre' \ + --tree_method 'clustalw' \ + --log_fp 'clustalw.txt' \ + --root_method 'tree_method_default' + +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'clearcut.tre' \ + --tree_method 'clearcut' \ + --log_fp 'clearcut.txt' \ + --root_method 'tree_method_default' + +make_phylogeny.py \ + --input_fp 'test-data/make_phylogeny/aligned.fasta' \ + --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \ + --tree_method 'fasttree' \ + --log_fp 'fasttree_midpoint.txt' \ + --root_method 'midpoint' + +# multiple_join_paired_ends +multiple_join_paired_ends.py \ + --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ + --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \ + --read1_indicator 'forward_' \ + --read2_indicator 'reverse_' \ + --leading_text '' \ + --trailing_text '' + +#multiple_join_paired_ends.py \ +# --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \ +# --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \ +# --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \ +# --read1_indicator '_R1_' \ +# --read2_indicator '_R2_' \ +# --leading_text '' \ +# --trailing_text '' + +multiple_join_paired_ends.py \ + --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \ + --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \ + --read1_indicator 'forward_' \ + --read2_indicator 'reverse_' \ + --match_barcodes \ + --barcode_indicator 'barcode_' \ + --leading_text '' \ + --trailing_text '' + +# multiple_split_libraries_fastq +multiple_split_libraries_fastq.py \ + --input_dir 'test-data/multiple_split_libraries_fastq/input' \ + --output_dir 'multiple_split_libraries_fastq' \ + --demultiplexing_method 'mapping_barcode_files' \ + --read_indicator 'reads_' \ + --barcode_indicator 'barcodes_' \ + --mapping_indicator 'mapping_' \ + --mapping_extensions 'txt' \ + --leading_text '' \ + --trailing_text '' \ + --sampleid_indicator '.' + +multiple_split_libraries_fastq.py \ + --input_dir 'test-data/multiple_split_libraries_fastq/input' \ + --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \ + --demultiplexing_method 'mapping_barcode_files' \ + --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \ + --read_indicator 'reads_' \ + --barcode_indicator 'barcodes_' \ + --mapping_indicator 'mapping_' \ + --mapping_extensions 'txt' \ + --leading_text '' \ + --trailing_text '' \ + --sampleid_indicator '.' + +# pick_closed_reference_otus +pick_closed_reference_otus.py \ + --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ + --output_dir 'pick_closed_reference_otus' \ + --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ + --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' +biom convert \ + -i 'pick_closed_reference_otus/otu_table.biom' \ + -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \ + --to-json + +pick_closed_reference_otus.py \ + --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ + --output_dir 'pick_closed_reference_otus_sortmerna' \ + --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ + --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \ + --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt' +biom convert \ + -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \ + -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \ + --to-json + +pick_closed_reference_otus.py \ + --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ + --output_dir 'pick_closed_reference_otus_assign_taxonomy' \ + --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ + --assign_taxonomy +biom convert \ + -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \ + -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \ + --to-json + +pick_closed_reference_otus.py \ + --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \ + --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \ + --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \ + --suppress_taxonomy_assignment +biom convert \ + -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \ + -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \ + --to-json + +# 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 + +# pick_otus +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_uclust' \ + --otu_picking_method 'uclust' \ + --similarity "0.97" \ + --denovo_otu_id_prefix "denovo" \ + --max_accepts "1" \ + --max_rejects "8" \ + --stepwords "8" \ + --word_length "8" \ + --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_sortmerna' \ + --otu_picking_method "sortmerna" \ + --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ + --sortmerna_e_value "1" \ + --sortmerna_coverage "0.97" \ + --sortmerna_tabular \ + --sortmerna_best_N_alignments "1" \ + --sortmerna_max_pos "10000" \ + --similarity "0.97" \ + --non_chimeras_retention "union" + +#pick_otus.py \ +# -i 'test-data/pick_otus/seqs.fna' \ +# -o 'pick_otus_mothur' \ +# --otu_picking_method "mothur" \ +# --clustering_algorithm "furthest" \ +# --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_trie' \ + --otu_picking_method "trie" \ + --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_uclust_ref' \ + --otu_picking_method "uclust_ref" \ + --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ + --similarity "0.97" \ + --max_accepts "1" \ + --max_rejects "8" \ + --stepwords "8" \ + --word_length "8" \ + --non_chimeras_retention "union" + +#pick_otus.py \ +# -i 'test-data/pick_otus/seqs.fna' \ +# -o 'pick_otus_blast' \ +# --otu_picking_method "blast" \ +# --refseqs_fp "test-data/pick_otus/refseqs.fasta" \ +# --similarity "0.97" \ +# --max_e_value_blast "1e-10" \ +# --min_aligned_percent "0.5" \ +# --non_chimeras_retention "union" + +# pick_otus.py \ +# -i 'test-data/pick_otus/seqs.fna' \ +# -o 'pick_otus_sumaclust' \ +# --otu_picking_method "sumaclust" \ +# --similarity "0.97" \ +# --sumaclust_l \ +# --denovo_otu_id_prefix "denovo" \ +# --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_swarm' \ + --otu_picking_method "swarm" \ + --denovo_otu_id_prefix "denovo" \ + --swarm_resolution "1" \ + --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_prefix_suffix' \ + --otu_picking_method "prefix_suffix" \ + --prefix_length "50" \ + --suffix_length "50" \ + --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_cdhit' \ + --otu_picking_method "cdhit" \ + --similarity "0.97" \ + --non_chimeras_retention "union" + +pick_otus.py \ + -i 'test-data/pick_otus/seqs.fna' \ + -o 'pick_otus_uclust_intersection' \ + --otu_picking_method "uclust" \ + --similarity "0.97" \ + --denovo_otu_id_prefix "denovo" \ + --max_accepts "1" \ + --max_rejects "8" \ + --stepwords "8" \ + --word_length "8" \ + --non_chimeras_retention "intersection" + +# pick_rep_set +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --rep_set_picking_method 'first' \ + --sort_by 'otu' \ + --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \ + --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt' + +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \ + --rep_set_picking_method 'first' \ + --sort_by 'otu' \ + --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \ + --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt' + +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --rep_set_picking_method 'longest' \ + --sort_by 'otu' \ + --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \ + --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt' + +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --rep_set_picking_method 'most_abundant' \ + --sort_by 'otu' \ + --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \ + --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt' + +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --rep_set_picking_method 'random' \ + --sort_by 'otu' \ + --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \ + --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt' + +pick_rep_set.py \ + --input_file 'test-data/pick_rep_set/seqs_otus.txt' \ + --fasta_file 'test-data/pick_rep_set/seqs.fna' \ + --rep_set_picking_method 'first' \ + --sort_by 'seq_id' \ + --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \ + --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt' + +# plot_taxa_summary +plot_taxa_summary.py \ + --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \ + --dir_path 'test-data/plot_taxa_summary/phylum' \ + --labels 'phylum' \ + --num_categories '20' \ + --background_color 'white' \ + --dpi '80' \ + --x_width '12' \ + --y_height '12' \ + --bar_width '0.75' \ + --type_of_file 'png' \ + --chart_type 'area,bar,pie' \ + --resize_nth_label '0' \ + --label_type 'categorical' + +plot_taxa_summary.py \ + --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \ + --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \ + --labels 'Phylum,Class,Genus' \ + --num_categories '20' \ + --background_color 'white' \ + --dpi '80' \ + --x_width '12' \ + --y_height '12' \ + --bar_width '0.75' \ + --type_of_file 'png' \ + --chart_type 'area,bar,pie' \ + --resize_nth_label '0' \ + --label_type 'categorical' + +plot_taxa_summary.py \ + --counts_fname 'test-data/plot_taxa_summary/class.txt' \ + --dir_path 'test-data/plot_taxa_summary/class' \ + --labels 'Class' \ + --num_categories '10' \ + --background_color 'white' \ + --dpi '80' \ + --x_width '12' \ + --y_height '12' \ + --bar_width '0.75' \ + --chart_type 'pie' \ + --type_of_file 'svg' \ + --include_html_legend \ + --resize_nth_label '0' \ + --label_type 'categorical' + +plot_taxa_summary.py \ + --counts_fname 'test-data/plot_taxa_summary/class.txt' \ + --dir_path 'test-data/plot_taxa_summary/class_colorby' \ + --labels 'Class' \ + --num_categories '20' \ + --colorby 'PC.636,PC.635' \ + --background_color 'white' \ + --dpi '80' \ + --x_width '12' \ + --y_height '12' \ + --bar_width '0.75' \ + --type_of_file 'pdf' \ + --chart_type 'area,bar,pie' \ + --resize_nth_label '0' \ + --label_type 'categorical' + +# 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 + +# 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 + +# 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 + +# summarize_taxa_through_plots +summarize_taxa_through_plots.py \ + --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ + --output_dir summarize_taxa_through_plots_mapping \ + --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' +biom convert \ + -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \ + -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \ + -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \ + -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \ + -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \ + -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \ + --to-json +cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/ +cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/ +cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html' +cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html' + +summarize_taxa_through_plots.py \ + --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ + --output_dir summarize_taxa_through_plots_mapping_categories \ + --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ + --mapping_category 'Treatment' +biom convert \ + -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \ + -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \ + -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \ + -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \ + -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \ + -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \ + --to-json +cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/ +cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/ +cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html' +cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html' + +summarize_taxa_through_plots.py \ + --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ + --output_dir summarize_taxa_through_plots_mapping_sort \ + --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \ + --sort +biom convert \ + -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \ + -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \ + -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \ + -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \ + -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \ + -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \ + --to-json +cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/ +cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/ +cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html' +cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html' + +summarize_taxa_through_plots.py \ + --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \ + --output_dir summarize_taxa_through_plots_without_mapping +biom convert \ + -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \ + -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \ + -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \ + -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \ + -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \ + --to-json +biom convert \ + -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \ + -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \ + --to-json +cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/ +cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/ +cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html' +cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html' + +# upgma_cluster +upgma_cluster.py \ + --input_path 'test-data/upgma_cluster/' \ + --output_path 'test-data/upgma_cluster/' + +# 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 + + + + + + + + + + + + + + + + + + +