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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:33:53 -0400
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1 #!/usr/bin/env bash
2
3 # Data are from test data in https://github.com/biocore/qiime
4
5 # align_seqs
6 align_seqs.py \
7 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
8 -o 'align_seqs_pynast_uclust' \
9 --alignment_method 'pynast' \
10 --pairwise_alignment_method 'uclust' \
11 --template_fp 'test-data/align_seqs/core_set_aligned.fasta.imputed' \
12 --min_percent_id '0.75'
13
14 align_seqs.py \
15 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
16 -o 'align_seqs_pynast_muscle' \
17 --alignment_method 'pynast' \
18 --pairwise_alignment_method 'muscle' \
19 --min_length '50' \
20 --min_percent_id '0.75'
21
22 align_seqs.py \
23 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
24 -o 'align_seqs_pynast_pair_hmm' \
25 --alignment_method 'pynast' \
26 --pairwise_alignment_method 'pair_hmm' \
27 --min_percent_id '0.75'
28
29 #align_seqs.py \
30 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
31 # -o 'align_seqs_pynast_clustal' \
32 # --alignment_method 'pynast' \
33 # --pairwise_alignment_method 'clustal' \
34 # --min_percent_id '0.75'
35
36 align_seqs.py \
37 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
38 -o 'align_seqs_pynast_blast' \
39 --alignment_method 'pynast' \
40 --pairwise_alignment_method 'blast' \
41 --min_percent_id '0.75'
42
43 align_seqs.py \
44 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
45 -o 'align_seqs_pynast_mafft' \
46 --alignment_method 'pynast' \
47 --pairwise_alignment_method 'mafft' \
48 --min_percent_id '0.75'
49
50 #align_seqs.py \
51 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
52 # -o 'align_seqs_infernal' \
53 # --alignment_method 'infernal' \
54 # --template_fp 'test-data/align_seqs/seed.16s.reference_model.sto' \
55 # --min_percent_id '0.75'
56
57 #align_seqs.py \
58 # --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
59 # -o 'align_seqs_clustalw' \
60 # --alignment_method 'clustalw' \
61 # --min_percent_id '0.75'
62
63 align_seqs.py \
64 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
65 -o 'align_seqs_muscle' \
66 --alignment_method 'muscle' \
67 --min_percent_id '0.75'
68
69 align_seqs.py \
70 --input_fasta_fp 'test-data/align_seqs/unaligned.fna' \
71 -o 'align_seqs_mafft' \
72 --alignment_method 'mafft' \
73 --min_percent_id '0.75'
74
75 #alpha_rarefaction
76 alpha_rarefaction.py \
77 --otu_table_fp "test-data/alpha_rarefaction/otu_table.biom" \
78 --mapping_fp "test-data/alpha_rarefaction/mapping_file.txt" \
79 -o alpha_rarefaction \
80 --num_steps '2' \
81 --tree_fp "test-data/alpha_rarefaction/rep_set.tre" \
82 --min_rare_depth '10' \
83 --max_rare_depth '50' \
84 --retain_intermediate_files
85 rm -rf alpha_rarefaction
86
87 # assign_taxonomy
88 assign_taxonomy.py \
89 --input_fasta_fp 'test-data/assign_taxonomy/uclust_input_seqs.fasta' \
90 --assignment_method 'uclust' \
91 --min_consensus_fraction '0.51' \
92 --similarity '0.9' \
93 --uclust_max_accepts '3' \
94 -o assign_taxonomy_uclust
95 cp assign_taxonomy_uclust/uclust_input_seqs_tax_assignments.txt 'test-data/assign_taxonomy/uclust_taxonomic_assignation.txt'
96 rm -rf assign_taxonomy_uclust
97
98 #assign_taxonomy.py \
99 # --input_fasta_fp 'test-data/assign_taxonomy/rdp_input_seqs.fasta' \
100 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rdp_id_to_taxonomy.txt' \
101 # --assignment_method 'rdp' \
102 # --confidence '3' \
103 # -o assign_taxonomy_rdp
104
105 #assign_taxonomy.py \
106 # --input_fasta_fp 'test-data/assign_taxonomy/rtax_ref_seq_set.fna' \
107 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/rtax_id_to_taxonomy.txt' \
108 # --assignment_method 'rtax' \
109 # --read_1_seqs_fp 'test-data/assign_taxonomy/read_1.seqs.fna' \
110 # --read_2_seqs_fp 'test-data/assign_taxonomy/read_2.seqs.fna' \
111 # --single_ok \
112 # --no_single_ok_generic \
113 # --read_id_regex "\S+\s+(\S+)" \
114 # --amplicon_id_regex "(\S+)\s+(\S+?)\/" \
115 # --header_id_regex "\S+\s+(\S+?)\/" \
116 # -o assign_taxonomy_rtax
117 #ls assign_taxonomy_rtax
118
119 #assign_taxonomy.py \
120 # --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
121 # --id_to_taxonomy_fp 'test-data/assign_taxonomy/mothur_id_to_taxonomy.txt' \
122 # --assignment_method 'mothur' \
123 # --confidence 0.5 \
124 # -o assign_taxonomy_mothur
125 #ls assign_taxonomy_mothur
126
127 assign_taxonomy.py \
128 --input_fasta_fp 'test-data/assign_taxonomy/mothur_ref_seq_set.fna' \
129 --assignment_method 'sortmerna' \
130 --min_consensus_fraction "0.51" \
131 --similarity "0.9" \
132 --sortmerna_e_value "1.0" \
133 --sortmerna_coverage "0.9" \
134 --sortmerna_best_N_alignments "5" \
135 -o assign_taxonomy_sortmerna
136 cp assign_taxonomy_sortmerna/sortmerna_map.blast 'test-data/assign_taxonomy/sortmerna_map.blast'
137 cp assign_taxonomy_sortmerna/mothur_ref_seq_set_tax_assignments.txt 'test-data/assign_taxonomy/sortmerna_taxonomic_assignation.txt'
138 rm -rf assign_taxonomy_sortmerna
139
140 #beta_diversity
141 beta_diversity.py \
142 --input_path 'test-data/beta_diversity/otu_table.biom' \
143 -o beta_diversity_1 \
144 --metrics 'unweighted_unifrac,weighted_unifrac' \
145 --tree_path 'test-data/beta_diversity/rep_set.tre'
146 md5 'beta_diversity_1/unweighted_unifrac_otu_table.txt'
147 md5 'beta_diversity_1/weighted_unifrac_otu_table.txt'
148 rm -rf beta_diversity_1
149
150 beta_diversity.py \
151 --input_path 'test-data/beta_diversity/otu_table.biom' \
152 -o beta_diversity_2 \
153 --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' \
154 --tree_path 'test-data/beta_diversity/rep_set.tre'
155 md5 'beta_diversity_2/canberra_otu_table.txt'
156 md5 'beta_diversity_2/pearson_otu_table.txt'
157 rm -rf beta_diversity_2
158
159 #beta_diversity_through_plots
160 beta_diversity_through_plots.py \
161 --otu_table_fp 'test-data/beta_diversity_through_plots/otu_table.biom' \
162 --mapping_fp 'test-data/beta_diversity_through_plots/map.txt' \
163 --output_dir beta_diversity_through_plots \
164 --tree_fp 'test-data/beta_diversity_through_plots/rep_set.tre' \
165 --parallel
166 cp beta_diversity_through_plots/unweighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
167 cp beta_diversity_through_plots/unweighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
168 cp beta_diversity_through_plots/weighted_unifrac_dm.txt 'test-data/beta_diversity_through_plots/'
169 cp beta_diversity_through_plots/weighted_unifrac_pc.txt 'test-data/beta_diversity_through_plots/'
170 rm -rf beta_diversity_through_plots
171
172 # compare_categories
173 compare_categories.py \
174 --method 'adonis' \
175 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
176 --mapping_file 'test-data/compare_categories/map.txt' \
177 --categories 'Treatment' \
178 -o compare_categories_1 \
179 --num_permutations '999'
180 cp compare_categories_1/adonis_results.txt "test-data/compare_categories/adonis_results.txt"
181 rm -rf compare_categories_1
182
183 compare_categories.py \
184 --method 'dbrda' \
185 --input_dm 'test-data/compare_categories/unweighted_unifrac_dm.txt' \
186 --mapping_file 'test-data/compare_categories/map.txt' \
187 --categories 'Treatment' \
188 -o compare_categories_2 \
189 --num_permutations '99'
190 cp compare_categories_2/* "test-data/compare_categories/"
191 rm -rf compare_categories_2
192
193 # core_diversity_analyses
194 core_diversity_analyses.py \
195 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
196 -o core_diversity_analyses_1 \
197 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
198 --sampling_depth 22 \
199 --tree_fp 'test-data/core_diversity_analyses/rep_set.tre'
200 cp core_diversity_analyses_1/bdiv_even22/unweighted_unifrac_pc.txt 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt'
201 rm -rf core_diversity_analyses_1
202
203 core_diversity_analyses.py \
204 --input_biom_fp 'test-data/core_diversity_analyses/otu_table.biom' \
205 -o core_diversity_analyses_2 \
206 --mapping_fp 'test-data/core_diversity_analyses/map.txt' \
207 --sampling_depth 22 \
208 --nonphylogenetic_diversity \
209 --suppress_taxa_summary \
210 --suppress_beta_diversity \
211 --suppress_alpha_diversity \
212 --suppress_group_significance
213 rm -rf core_diversity_analyses_2
214
215 # filter_alignment
216 filter_alignment.py \
217 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
218 -o 'filter_alignment_default' \
219 --allowed_gap_frac '0.999999' \
220 --threshold '3.0'
221
222 filter_alignment.py \
223 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
224 -o 'filter_alignment_without_mask_filter_and_outliers' \
225 --suppress_lane_mask_filter \
226 --allowed_gap_frac '0.999999' \
227 --remove_outliers \
228 --threshold '3.0'
229
230 filter_alignment.py \
231 --input_fasta_file 'test-data/filter_alignment/alignment.fasta' \
232 -o 'filter_alignment_entropy' \
233 --allowed_gap_frac '0.999999' \
234 --threshold '3.0' \
235 --entropy_threshold '0.1'
236
237 # filter_fasta
238 filter_fasta.py \
239 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
240 --output_fasta_fp 'filter_fasta_otu_map.fasta' \
241 --otu_map 'test-data/filter_fasta/otu_map.txt'
242
243 filter_fasta.py \
244 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
245 --output_fasta_fp 'filter_fasta_otu_map_negate.fasta' \
246 --otu_map 'test-data/filter_fasta/otu_map.txt' \
247 --negate
248
249 filter_fasta.py \
250 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
251 --output_fasta_fp 'filter_fasta_seq_id.fasta' \
252 --seq_id_fp 'test-data/filter_fasta/seqs_to_keep.txt'
253
254 filter_fasta.py \
255 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
256 --output_fasta_fp 'filter_fasta_otu_table.fasta' \
257 --biom_fp 'test-data/filter_fasta/otu_table.biom'
258
259 filter_fasta.py \
260 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
261 --output_fasta_fp 'filter_fasta_subject_fasta.fasta' \
262 --subject_fasta_fp 'test-data/filter_fasta/sl_inseqs.fasta'
263
264 filter_fasta.py \
265 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
266 --output_fasta_fp 'filter_fasta_seq_id_prefix.fasta' \
267 --seq_id_prefix 'S5'
268
269 filter_fasta.py \
270 --input_fasta_fp 'test-data/filter_fasta/inseqs.fasta' \
271 --output_fasta_fp 'filter_fasta_sample_id.fasta' \
272 --sample_id_fp 'test-data/filter_fasta/map.txt'
273
274 # filter_otus_from_otu_table
275 filter_otus_from_otu_table.py \
276 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
277 --min_count '2' \
278 --max_count '1000' \
279 --min_samples '5' \
280 --max_samples '350' \
281 --output_fp 'test-data/filter_otus_from_otu_table/filtered_otu_table.biom'
282
283 filter_otus_from_otu_table.py \
284 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
285 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
286 --output_fp 'test-data/filter_otus_from_otu_table/chimera_filtered_otu_table.biom'
287
288 filter_otus_from_otu_table.py \
289 --input_fp 'test-data/filter_otus_from_otu_table/otu_table.biom' \
290 --otu_ids_to_exclude_fp 'test-data/filter_otus_from_otu_table/chimeric_otus.txt' \
291 --negate_ids_to_exclude \
292 --output_fp 'test-data/filter_otus_from_otu_table/chimera_picked_otu_table.biom'
293
294 # filter_samples_from_otu_table
295 filter_samples_from_otu_table.py \
296 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
297 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
298 --min_count '150'
299 biom convert \
300 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
301 -o 'test-data/filter_samples_from_otu_table/abundance_min.biom' \
302 --to-json
303 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
304
305 filter_samples_from_otu_table.py \
306 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
307 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
308 --min_count '0' \
309 --max_count '149'
310 biom convert \
311 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
312 -o 'test-data/filter_samples_from_otu_table/abundance_max.biom' \
313 --to-json
314 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
315
316 filter_samples_from_otu_table.py \
317 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
318 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
319 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
320 --output_mapping_fp 'test-data/filter_samples_from_otu_table/metadata_positive.txt' \
321 -s 'Treatment:Control'
322 biom convert \
323 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
324 -o 'test-data/filter_samples_from_otu_table/metadata_positive.biom' \
325 --to-json
326 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
327
328 filter_samples_from_otu_table.py \
329 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
330 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
331 --mapping_fp 'test-data/filter_samples_from_otu_table/map.txt' \
332 -s 'Treatment:*,!Control'
333 biom convert \
334 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
335 -o 'test-data/filter_samples_from_otu_table/metadata_negative.biom' \
336 --to-json
337 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
338
339 filter_samples_from_otu_table.py \
340 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
341 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
342 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt'
343 biom convert \
344 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
345 -o 'test-data/filter_samples_from_otu_table/id_positive.biom' \
346 --to-json
347 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
348
349 filter_samples_from_otu_table.py \
350 --input_fp 'test-data/filter_samples_from_otu_table/otu_table.biom' \
351 --output_fp 'test-data/filter_samples_from_otu_table/tmp.biom' \
352 --sample_id_fp 'test-data/filter_samples_from_otu_table/ids.txt' \
353 --negate_sample_id_fp
354 biom convert \
355 -i 'test-data/filter_samples_from_otu_table/tmp.biom' \
356 -o 'test-data/filter_samples_from_otu_table/id_negative.biom' \
357 --to-json
358 rm 'test-data/filter_samples_from_otu_table/tmp.biom'
359
360 # filter_taxa_from_otu_table
361 filter_taxa_from_otu_table.py \
362 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
363 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
364 --positive_taxa 'p__Bacteroidetes,p__Firmicutes' \
365 --metadata_field 'taxonomy'
366 biom convert \
367 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
368 -o 'test-data/filter_taxa_from_otu_table/positive_taxa.biom' \
369 --to-json
370 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
371
372 filter_taxa_from_otu_table.py \
373 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
374 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
375 --negative_taxa 'p__Bacteroidetes,p__Firmicutes' \
376 --metadata_field 'taxonomy'
377 biom convert \
378 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
379 -o 'test-data/filter_taxa_from_otu_table/negative_taxa.biom' \
380 --to-json
381 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
382
383 filter_taxa_from_otu_table.py \
384 --input_otu_table_fp 'test-data/filter_taxa_from_otu_table/otu_table.biom' \
385 --output_otu_table_fp 'test-data/filter_taxa_from_otu_table/tmp.biom' \
386 --positive_taxa 'p__Firmicutes' \
387 --negative_taxa 'c__Clostridia' \
388 --metadata_field 'taxonomy'
389 biom convert \
390 -i 'test-data/filter_taxa_from_otu_table/tmp.biom' \
391 -o 'test-data/filter_taxa_from_otu_table/positive_negative_taxa.biom' \
392 --to-json
393 rm 'test-data/filter_taxa_from_otu_table/tmp.biom'
394
395 # jackknifed_beta_diversity
396 jackknifed_beta_diversity.py \
397 --otu_table_fp 'test-data/jackknifed_beta_diversity/otu_table.biom' \
398 --mapping_fp 'test-data/jackknifed_beta_diversity/map.txt' \
399 -o jackknifed_beta_diversity \
400 --seqs_per_sample '10' \
401 --tree_fp 'test-data/jackknifed_beta_diversity/rep_set.tre' \
402 --master_tree 'consensus' \
403 --parallel
404 rm -rf jackknifed_beta_diversity
405
406 # make_emperor
407 cp 'test-data/core_diversity_analyses/unweighted_unifrac_pc.txt' 'test-data/make_emperor/unweighted_unifrac_pc.txt'
408 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/make_emperor/map.txt'
409 cp 'test-data/summarize_taxa/2_L3.txt' 'test-data/make_emperor/2_L3.txt'
410
411 make_emperor.py \
412 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
413 -o make_emperor_1 \
414 --map_fp 'test-data/make_emperor/map.txt' \
415 --number_of_axes '10' \
416 --add_unique_columns \
417 --number_of_segments 8
418 rm -rf make_emperor_1
419
420 make_emperor.py \
421 --input_coords 'test-data/make_emperor/unweighted_unifrac_pc.txt' \
422 -o make_emperor_2 \
423 --map_fp 'test-data/make_emperor/map.txt' \
424 --number_of_axes '10' \
425 --add_unique_columns \
426 --number_of_segments 8 \
427 --taxa_fp 'test-data/make_emperor/2_L3.txt' \
428 --n_taxa_to_keep 10
429 rm -rf make_emperor_2
430
431 # make_otu_heatmap
432 make_otu_heatmap.py \
433 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
434 --imagetype 'pdf' \
435 --color_scheme "YlGn" \
436 --width "5" \
437 --height "5" \
438 --dpi "200" \
439 --obs_md_category "taxonomy" \
440 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.pdf'
441
442 make_otu_heatmap.py \
443 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
444 --imagetype 'png' \
445 --color_scheme "YlGn" \
446 --width "5" \
447 --height "5" \
448 --dpi "200" \
449 --obs_md_category "taxonomy" \
450 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.png'
451
452 make_otu_heatmap.py \
453 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
454 --imagetype 'svg' \
455 --color_scheme "YlGn" \
456 --width "5" \
457 --height "5" \
458 --dpi "200" \
459 --obs_md_category "taxonomy" \
460 --output_fp 'test-data/make_otu_heatmap/basic_heatmap.svg'
461
462 make_otu_heatmap.py \
463 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
464 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
465 --imagetype 'pdf' \
466 --color_scheme "YlGn" \
467 --width "5" \
468 --height "5" \
469 --dpi "200" \
470 --obs_md_category "taxonomy" \
471 --output_fp 'test-data/make_otu_heatmap/sample_sorted_heatmap.pdf'
472
473 make_otu_heatmap.py \
474 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
475 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
476 --otu_tree 'test-data/make_otu_heatmap/rep_set.tre' \
477 --imagetype 'pdf' \
478 --color_scheme "YlGn" \
479 --width "5" \
480 --height "5" \
481 --dpi "200" \
482 --obs_md_category "taxonomy" \
483 --output_fp 'test-data/make_otu_heatmap/sample_otu_sorted_heatmap.pdf'
484
485 make_otu_heatmap.py \
486 --otu_table_fp 'test-data/make_otu_heatmap/otu_table.biom' \
487 --map_fname 'test-data/make_otu_heatmap/mapping_file.txt' \
488 --category "Treatment" \
489 --imagetype 'pdf' \
490 --color_scheme "YlGn" \
491 --width "5" \
492 --height "5" \
493 --dpi "200" \
494 --obs_md_category "taxonomy" \
495 --output_fp 'test-data/make_otu_heatmap/treatment_sample_sorted_heatmap.pdf'
496
497 # make_phylogeny
498 make_phylogeny.py \
499 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
500 --result_fp 'test-data/make_phylogeny/fasttree_tree_method_default.tre' \
501 --tree_method 'fasttree' \
502 --log_fp 'fasttree_tree_method_default.txt' \
503 --root_method 'tree_method_default'
504
505 make_phylogeny.py \
506 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
507 --result_fp 'raxml_v730.tre' \
508 --tree_method 'raxml_v730' \
509 --log_fp 'raxml_v730.txt' \
510 --root_method 'tree_method_default'
511
512 make_phylogeny.py \
513 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
514 --result_fp 'test-data/make_phylogeny/muscle.tre' \
515 --tree_method 'muscle' \
516 --log_fp 'muscle.txt' \
517 --root_method 'tree_method_default'
518
519 make_phylogeny.py \
520 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
521 --result_fp 'test-data/make_phylogeny/clustalw.tre' \
522 --tree_method 'clustalw' \
523 --log_fp 'clustalw.txt' \
524 --root_method 'tree_method_default'
525
526 make_phylogeny.py \
527 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
528 --result_fp 'clearcut.tre' \
529 --tree_method 'clearcut' \
530 --log_fp 'clearcut.txt' \
531 --root_method 'tree_method_default'
532
533 make_phylogeny.py \
534 --input_fp 'test-data/make_phylogeny/aligned.fasta' \
535 --result_fp 'test-data/make_phylogeny/fasttree_midpoint.tre' \
536 --tree_method 'fasttree' \
537 --log_fp 'fasttree_midpoint.txt' \
538 --root_method 'midpoint'
539
540 # multiple_join_paired_ends
541 multiple_join_paired_ends.py \
542 --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
543 --output_dir 'test-data/multiple_join_paired_ends/output_without_barcode' \
544 --read1_indicator 'forward_' \
545 --read2_indicator 'reverse_' \
546 --leading_text '' \
547 --trailing_text ''
548
549 #multiple_join_paired_ends.py \
550 # --input_dir 'test-data/multiple_join_paired_ends/without_barcode/' \
551 # --output_dir 'multiple_join_paired_ends_without_barcode_parameter_files' \
552 # --parameter_fp 'test-data/multiple_join_paired_ends/qiime_parameters.txt' \
553 # --read1_indicator '_R1_' \
554 # --read2_indicator '_R2_' \
555 # --leading_text '' \
556 # --trailing_text ''
557
558 multiple_join_paired_ends.py \
559 --input_dir 'test-data/multiple_join_paired_ends/with_barcode/' \
560 --output_dir 'test-data/multiple_join_paired_ends/output_with_barcode' \
561 --read1_indicator 'forward_' \
562 --read2_indicator 'reverse_' \
563 --match_barcodes \
564 --barcode_indicator 'barcode_' \
565 --leading_text '' \
566 --trailing_text ''
567
568 # multiple_split_libraries_fastq
569 multiple_split_libraries_fastq.py \
570 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
571 --output_dir 'multiple_split_libraries_fastq' \
572 --demultiplexing_method 'mapping_barcode_files' \
573 --read_indicator 'reads_' \
574 --barcode_indicator 'barcodes_' \
575 --mapping_indicator 'mapping_' \
576 --mapping_extensions 'txt' \
577 --leading_text '' \
578 --trailing_text '' \
579 --sampleid_indicator '.'
580
581 multiple_split_libraries_fastq.py \
582 --input_dir 'test-data/multiple_split_libraries_fastq/input' \
583 --output_dir 'multiple_split_libraries_fastq_with_parameter_file' \
584 --demultiplexing_method 'mapping_barcode_files' \
585 --parameter_fp 'test-data/multiple_split_libraries_fastq/qiime_parameters.txt' \
586 --read_indicator 'reads_' \
587 --barcode_indicator 'barcodes_' \
588 --mapping_indicator 'mapping_' \
589 --mapping_extensions 'txt' \
590 --leading_text '' \
591 --trailing_text '' \
592 --sampleid_indicator '.'
593
594 # pick_closed_reference_otus
595 pick_closed_reference_otus.py \
596 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
597 --output_dir 'pick_closed_reference_otus' \
598 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
599 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt'
600 biom convert \
601 -i 'pick_closed_reference_otus/otu_table.biom' \
602 -o 'test-data/pick_closed_reference_otus/basic_otu_table.biom' \
603 --to-json
604
605 pick_closed_reference_otus.py \
606 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
607 --output_dir 'pick_closed_reference_otus_sortmerna' \
608 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
609 --taxonomy_fp 'test-data/pick_closed_reference_otus/taxa.txt' \
610 --parameter_fp 'test-data/pick_closed_reference_otus/sortmerna_params.txt'
611 biom convert \
612 -i 'pick_closed_reference_otus_sortmerna/otu_table.biom' \
613 -o 'test-data/pick_closed_reference_otus/sortmerna_otu_table.biom' \
614 --to-json
615
616 pick_closed_reference_otus.py \
617 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
618 --output_dir 'pick_closed_reference_otus_assign_taxonomy' \
619 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
620 --assign_taxonomy
621 biom convert \
622 -i 'pick_closed_reference_otus_assign_taxonomy/otu_table.biom' \
623 -o 'test-data/pick_closed_reference_otus/assign_taxonomy_otu_table.biom' \
624 --to-json
625
626 pick_closed_reference_otus.py \
627 --input_fp 'test-data/pick_closed_reference_otus/seqs.fna' \
628 --output_dir 'pick_closed_reference_otus_suppress_taxonomy_assignment' \
629 --reference_fp 'test-data/pick_closed_reference_otus/refseqs.fna' \
630 --suppress_taxonomy_assignment
631 biom convert \
632 -i 'pick_closed_reference_otus_suppress_taxonomy_assignment/otu_table.biom' \
633 -o 'test-data/pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom' \
634 --to-json
635
636 # pick_open_reference_otus
637 pick_open_reference_otus.py \
638 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
639 -o pick_open_reference_otus_1 \
640 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
641 --otu_picking_method 'uclust' \
642 --new_ref_set_id 'New' \
643 --parallel \
644 --percent_subsample '0.001' \
645 --prefilter_percent_id '0.0' \
646 --minimum_failure_threshold '100000' \
647 --min_otu_size '2'
648 cp pick_open_reference_otus_1/final_otu_map.txt 'test-data/pick_open_reference_otus/1_final_otu_map.txt'
649 cp pick_open_reference_otus_1/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/1_final_otu_map_mc.txt'
650 cp pick_open_reference_otus_1/rep_set.tre 'test-data/pick_open_reference_otus/1_rep_set_tree.tre'
651 rm -rf pick_open_reference_otus_1
652
653 pick_open_reference_otus.py \
654 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
655 -o pick_open_reference_otus_2 \
656 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
657 --otu_picking_method 'uclust' \
658 --new_ref_set_id 'New' \
659 --parallel \
660 --percent_subsample '0.001' \
661 --prefilter_percent_id '0.0' \
662 --minimum_failure_threshold '100000' \
663 --min_otu_size '3' \
664 --suppress_taxonomy_assignment \
665 --suppress_align_and_tree
666 cp pick_open_reference_otus_2/final_otu_map.txt 'test-data/pick_open_reference_otus/2_final_otu_map.txt'
667 cp pick_open_reference_otus_2/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/2_final_otu_map_mc.txt'
668 rm -rf pick_open_reference_otus_2
669
670 pick_open_reference_otus.py \
671 --input_fps 'test-data/pick_open_reference_otus/sequences.fasta' \
672 -o pick_open_reference_otus_3 \
673 --reference_fp 'test-data/gg_13_8_79_otus.fasta' \
674 --otu_picking_method 'uclust' \
675 --new_ref_set_id 'New' \
676 --parallel \
677 --percent_subsample '0.001' \
678 --prefilter_percent_id '0.0' \
679 --minimum_failure_threshold '100000' \
680 --min_otu_size '10' \
681 --suppress_taxonomy_assignment
682 cp pick_open_reference_otus_3/final_otu_map.txt 'test-data/pick_open_reference_otus/3_final_otu_map.txt'
683 cp pick_open_reference_otus_3/final_otu_map_mc*.txt 'test-data/pick_open_reference_otus/3_final_otu_map_mc.txt'
684 cp pick_open_reference_otus_3/rep_set.tre 'test-data/pick_open_reference_otus/3_rep_set_tree.tre'
685 rm -rf pick_open_reference_otus_3
686
687 # pick_otus
688 pick_otus.py \
689 -i 'test-data/pick_otus/seqs.fna' \
690 -o 'pick_otus_uclust' \
691 --otu_picking_method 'uclust' \
692 --similarity "0.97" \
693 --denovo_otu_id_prefix "denovo" \
694 --max_accepts "1" \
695 --max_rejects "8" \
696 --stepwords "8" \
697 --word_length "8" \
698 --non_chimeras_retention "union"
699
700 pick_otus.py \
701 -i 'test-data/pick_otus/seqs.fna' \
702 -o 'pick_otus_sortmerna' \
703 --otu_picking_method "sortmerna" \
704 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
705 --sortmerna_e_value "1" \
706 --sortmerna_coverage "0.97" \
707 --sortmerna_tabular \
708 --sortmerna_best_N_alignments "1" \
709 --sortmerna_max_pos "10000" \
710 --similarity "0.97" \
711 --non_chimeras_retention "union"
712
713 #pick_otus.py \
714 # -i 'test-data/pick_otus/seqs.fna' \
715 # -o 'pick_otus_mothur' \
716 # --otu_picking_method "mothur" \
717 # --clustering_algorithm "furthest" \
718 # --non_chimeras_retention "union"
719
720 pick_otus.py \
721 -i 'test-data/pick_otus/seqs.fna' \
722 -o 'pick_otus_trie' \
723 --otu_picking_method "trie" \
724 --non_chimeras_retention "union"
725
726 pick_otus.py \
727 -i 'test-data/pick_otus/seqs.fna' \
728 -o 'pick_otus_uclust_ref' \
729 --otu_picking_method "uclust_ref" \
730 --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
731 --similarity "0.97" \
732 --max_accepts "1" \
733 --max_rejects "8" \
734 --stepwords "8" \
735 --word_length "8" \
736 --non_chimeras_retention "union"
737
738 #pick_otus.py \
739 # -i 'test-data/pick_otus/seqs.fna' \
740 # -o 'pick_otus_blast' \
741 # --otu_picking_method "blast" \
742 # --refseqs_fp "test-data/pick_otus/refseqs.fasta" \
743 # --similarity "0.97" \
744 # --max_e_value_blast "1e-10" \
745 # --min_aligned_percent "0.5" \
746 # --non_chimeras_retention "union"
747
748 # pick_otus.py \
749 # -i 'test-data/pick_otus/seqs.fna' \
750 # -o 'pick_otus_sumaclust' \
751 # --otu_picking_method "sumaclust" \
752 # --similarity "0.97" \
753 # --sumaclust_l \
754 # --denovo_otu_id_prefix "denovo" \
755 # --non_chimeras_retention "union"
756
757 pick_otus.py \
758 -i 'test-data/pick_otus/seqs.fna' \
759 -o 'pick_otus_swarm' \
760 --otu_picking_method "swarm" \
761 --denovo_otu_id_prefix "denovo" \
762 --swarm_resolution "1" \
763 --non_chimeras_retention "union"
764
765 pick_otus.py \
766 -i 'test-data/pick_otus/seqs.fna' \
767 -o 'pick_otus_prefix_suffix' \
768 --otu_picking_method "prefix_suffix" \
769 --prefix_length "50" \
770 --suffix_length "50" \
771 --non_chimeras_retention "union"
772
773 pick_otus.py \
774 -i 'test-data/pick_otus/seqs.fna' \
775 -o 'pick_otus_cdhit' \
776 --otu_picking_method "cdhit" \
777 --similarity "0.97" \
778 --non_chimeras_retention "union"
779
780 pick_otus.py \
781 -i 'test-data/pick_otus/seqs.fna' \
782 -o 'pick_otus_uclust_intersection' \
783 --otu_picking_method "uclust" \
784 --similarity "0.97" \
785 --denovo_otu_id_prefix "denovo" \
786 --max_accepts "1" \
787 --max_rejects "8" \
788 --stepwords "8" \
789 --word_length "8" \
790 --non_chimeras_retention "intersection"
791
792 # pick_rep_set
793 pick_rep_set.py \
794 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
795 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
796 --rep_set_picking_method 'first' \
797 --sort_by 'otu' \
798 --result_fp 'test-data/pick_rep_set/first_otu_fasta.fasta' \
799 --log_fp 'test-data/pick_rep_set/first_otu_fasta.txt'
800
801 pick_rep_set.py \
802 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
803 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
804 --reference_seqs_fp 'test-data/pick_rep_set/refseqs.fasta' \
805 --rep_set_picking_method 'first' \
806 --sort_by 'otu' \
807 --result_fp 'test-data/pick_rep_set/first_otu_fasta_ref.fasta' \
808 --log_fp 'test-data/pick_rep_set/first_otu_fasta_ref.txt'
809
810 pick_rep_set.py \
811 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
812 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
813 --rep_set_picking_method 'longest' \
814 --sort_by 'otu' \
815 --result_fp 'test-data/pick_rep_set/longest_otu_fasta.fasta' \
816 --log_fp 'test-data/pick_rep_set/longest_otu_fasta.txt'
817
818 pick_rep_set.py \
819 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
820 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
821 --rep_set_picking_method 'most_abundant' \
822 --sort_by 'otu' \
823 --result_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.fasta' \
824 --log_fp 'test-data/pick_rep_set/most_abundant_otu_fasta.txt'
825
826 pick_rep_set.py \
827 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
828 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
829 --rep_set_picking_method 'random' \
830 --sort_by 'otu' \
831 --result_fp 'test-data/pick_rep_set/random_otu_fasta.fasta' \
832 --log_fp 'test-data/pick_rep_set/random_otu_fasta.txt'
833
834 pick_rep_set.py \
835 --input_file 'test-data/pick_rep_set/seqs_otus.txt' \
836 --fasta_file 'test-data/pick_rep_set/seqs.fna' \
837 --rep_set_picking_method 'first' \
838 --sort_by 'seq_id' \
839 --result_fp 'test-data/pick_rep_set/first_seq_id_fasta.fasta' \
840 --log_fp 'test-data/pick_rep_set/first_seq_id_fasta.txt'
841
842 # plot_taxa_summary
843 plot_taxa_summary.py \
844 --counts_fname 'test-data/plot_taxa_summary/phylum.txt' \
845 --dir_path 'test-data/plot_taxa_summary/phylum' \
846 --labels 'phylum' \
847 --num_categories '20' \
848 --background_color 'white' \
849 --dpi '80' \
850 --x_width '12' \
851 --y_height '12' \
852 --bar_width '0.75' \
853 --type_of_file 'png' \
854 --chart_type 'area,bar,pie' \
855 --resize_nth_label '0' \
856 --label_type 'categorical'
857
858 plot_taxa_summary.py \
859 --counts_fname 'test-data/plot_taxa_summary/phylum.txt,test-data/plot_taxa_summary/class.txt,test-data/plot_taxa_summary/genus.txt' \
860 --dir_path 'test-data/plot_taxa_summary/phylum_class_genus' \
861 --labels 'Phylum,Class,Genus' \
862 --num_categories '20' \
863 --background_color 'white' \
864 --dpi '80' \
865 --x_width '12' \
866 --y_height '12' \
867 --bar_width '0.75' \
868 --type_of_file 'png' \
869 --chart_type 'area,bar,pie' \
870 --resize_nth_label '0' \
871 --label_type 'categorical'
872
873 plot_taxa_summary.py \
874 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
875 --dir_path 'test-data/plot_taxa_summary/class' \
876 --labels 'Class' \
877 --num_categories '10' \
878 --background_color 'white' \
879 --dpi '80' \
880 --x_width '12' \
881 --y_height '12' \
882 --bar_width '0.75' \
883 --chart_type 'pie' \
884 --type_of_file 'svg' \
885 --include_html_legend \
886 --resize_nth_label '0' \
887 --label_type 'categorical'
888
889 plot_taxa_summary.py \
890 --counts_fname 'test-data/plot_taxa_summary/class.txt' \
891 --dir_path 'test-data/plot_taxa_summary/class_colorby' \
892 --labels 'Class' \
893 --num_categories '20' \
894 --colorby 'PC.636,PC.635' \
895 --background_color 'white' \
896 --dpi '80' \
897 --x_width '12' \
898 --y_height '12' \
899 --bar_width '0.75' \
900 --type_of_file 'pdf' \
901 --chart_type 'area,bar,pie' \
902 --resize_nth_label '0' \
903 --label_type 'categorical'
904
905 # split_libraries
906 split_libraries.py \
907 --map 'test-data/split_libraries/mapping_file.txt' \
908 -o split_libraries \
909 --fasta 'test-data/split_libraries/reads_1.fna,test-data/split_libraries/reads_2.fna' \
910 --qual 'test-data/split_libraries/reads_1.qual,test-data/split_libraries/reads_2.qual' \
911 --min_qual_score 25 \
912 --qual_score_window 0 \
913 --record_qual_scores \
914 --min_seq_length 200 \
915 --max_seq_length 1000 \
916 --max_ambig 6 \
917 --max_homopolymer 6 \
918 --max_primer_mismatch 0 \
919 --barcode_type 'golay_12' \
920 --max_barcode_errors 1.5 \
921 --start_numbering_at 1
922 cp split_libraries/seqs.fna 'test-data/split_libraries/seqs.fna'
923 cp split_libraries/split_library_log.txt 'test-data/split_libraries/split_library_log'
924 cp split_libraries/histograms.txt 'test-data/split_libraries/histograms.txt'
925 cp split_libraries/seqs_filtered.qual 'test-data/split_libraries/seqs_filtered.qual'
926 rm -rf split_libraries
927
928 # split_libraries_fastq
929 split_libraries_fastq.py \
930 --sequence_read_fps 'test-data/split_libraries_fastq/forward_reads.fastq' \
931 -o split_libraries \
932 --mapping_fps 'test-data/map.tsv' \
933 --barcode_read_fps 'test-data/split_libraries_fastq/barcodes.fastq' \
934 --store_qual_scores \
935 --store_demultiplexed_fastq \
936 --max_bad_run_length 3 \
937 --min_per_read_length_fraction 0.75 \
938 --sequence_max_n 0 \
939 --start_seq_id 0 \
940 --barcode_type 'golay_12' \
941 --max_barcode_errors 1.5
942 cp split_libraries/histograms.txt 'test-data/split_libraries_fastq/histograms.tabular'
943 cp split_libraries/seqs.fna 'test-data/split_libraries_fastq/sequences.fasta'
944 cp split_libraries/seqs.qual 'test-data/split_libraries_fastq/sequence_qualities.qual'
945 cp split_libraries/seqs.fastq 'test-data/split_libraries_fastq/demultiplexed_sequences.fastq'
946 rm -rf split_libraries
947
948 # summarize_taxa
949 cp 'test-data/core_diversity_analyses/otu_table.biom' 'test-data/summarize_taxa/otu_table.biom'
950 cp 'test-data/core_diversity_analyses/map.txt' 'test-data/summarize_taxa/map.txt'
951
952 summarize_taxa.py \
953 -i 'test-data/summarize_taxa/otu_table.biom' \
954 -o summarize_taxa_1 \
955 -L '2,3,4,5,6' \
956 -m 'test-data/summarize_taxa/map.txt' \
957 --md_identifier "taxonomy" \
958 --delimiter ";"
959 cp summarize_taxa_1/*_L2.txt "test-data/summarize_taxa/1_L2.txt"
960 cp summarize_taxa_1/*_L3.txt "test-data/summarize_taxa/1_L3.txt"
961 cp summarize_taxa_1/*_L4.txt "test-data/summarize_taxa/1_L4.txt"
962 cp summarize_taxa_1/*_L5.txt "test-data/summarize_taxa/1_L5.txt"
963 cp summarize_taxa_1/*_L6.txt "test-data/summarize_taxa/1_L6.txt"
964 rm -rf summarize_taxa_1
965
966 summarize_taxa.py \
967 -i 'test-data/summarize_taxa/otu_table.biom' \
968 -o summarize_taxa_2 \
969 -L '3,6' \
970 --md_identifier "taxonomy" \
971 --delimiter ";"
972 cp summarize_taxa_2/*_L3.txt "test-data/summarize_taxa/2_L3.txt"
973 cp summarize_taxa_2/*_L6.txt "test-data/summarize_taxa/2_L6.txt"
974 rm -rf summarize_taxa_2
975
976 # summarize_taxa_through_plots
977 summarize_taxa_through_plots.py \
978 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
979 --output_dir summarize_taxa_through_plots_mapping \
980 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt'
981 biom convert \
982 -i 'summarize_taxa_through_plots_mapping/otu_table_L2.biom' \
983 -o 'summarize_taxa_through_plots_mapping/otu_table_L2_json.biom' \
984 --to-json
985 biom convert \
986 -i 'summarize_taxa_through_plots_mapping/otu_table_L3.biom' \
987 -o 'summarize_taxa_through_plots_mapping/otu_table_L3_json.biom' \
988 --to-json
989 biom convert \
990 -i 'summarize_taxa_through_plots_mapping/otu_table_L4.biom' \
991 -o 'summarize_taxa_through_plots_mapping/otu_table_L4_json.biom' \
992 --to-json
993 biom convert \
994 -i 'summarize_taxa_through_plots_mapping/otu_table_L5.biom' \
995 -o 'summarize_taxa_through_plots_mapping/otu_table_L5_json.biom' \
996 --to-json
997 biom convert \
998 -i 'summarize_taxa_through_plots_mapping/otu_table_L6.biom' \
999 -o 'summarize_taxa_through_plots_mapping/otu_table_L6_json.biom' \
1000 --to-json
1001 cp summarize_taxa_through_plots_mapping/*.txt test-data/summarize_taxa_through_plots/mapping/
1002 cp summarize_taxa_through_plots_mapping/*_json.biom test-data/summarize_taxa_through_plots/mapping/
1003 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping/area_charts.html'
1004 cp summarize_taxa_through_plots_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping/bar_charts.html'
1005
1006 summarize_taxa_through_plots.py \
1007 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
1008 --output_dir summarize_taxa_through_plots_mapping_categories \
1009 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
1010 --mapping_category 'Treatment'
1011 biom convert \
1012 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2.biom' \
1013 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L2_json.biom' \
1014 --to-json
1015 biom convert \
1016 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3.biom' \
1017 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L3_json.biom' \
1018 --to-json
1019 biom convert \
1020 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4.biom' \
1021 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L4_json.biom' \
1022 --to-json
1023 biom convert \
1024 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5.biom' \
1025 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L5_json.biom' \
1026 --to-json
1027 biom convert \
1028 -i 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6.biom' \
1029 -o 'summarize_taxa_through_plots_mapping_categories/Treatment_otu_table_L6_json.biom' \
1030 --to-json
1031 cp summarize_taxa_through_plots_mapping_categories/*.txt test-data/summarize_taxa_through_plots/mapping_categories/
1032 cp summarize_taxa_through_plots_mapping_categories/*_json.biom test-data/summarize_taxa_through_plots/mapping_categories/
1033 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/area_charts.html'
1034 cp summarize_taxa_through_plots_mapping_categories/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_categories/bar_charts.html'
1035
1036 summarize_taxa_through_plots.py \
1037 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
1038 --output_dir summarize_taxa_through_plots_mapping_sort \
1039 --mapping_fp 'test-data/summarize_taxa_through_plots/Fasting_Map.txt' \
1040 --sort
1041 biom convert \
1042 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2.biom' \
1043 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L2_json.biom' \
1044 --to-json
1045 biom convert \
1046 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3.biom' \
1047 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L3_json.biom' \
1048 --to-json
1049 biom convert \
1050 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4.biom' \
1051 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L4_json.biom' \
1052 --to-json
1053 biom convert \
1054 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5.biom' \
1055 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L5_json.biom' \
1056 --to-json
1057 biom convert \
1058 -i 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6.biom' \
1059 -o 'summarize_taxa_through_plots_mapping_sort/otu_table_sorted_L6_json.biom' \
1060 --to-json
1061 cp summarize_taxa_through_plots_mapping_sort/*.txt test-data/summarize_taxa_through_plots/mapping_sort/
1062 cp summarize_taxa_through_plots_mapping_sort/*_json.biom test-data/summarize_taxa_through_plots/mapping_sort/
1063 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/area_charts.html'
1064 cp summarize_taxa_through_plots_mapping_sort/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/mapping_sort/bar_charts.html'
1065
1066 summarize_taxa_through_plots.py \
1067 --otu_table_fp 'test-data/summarize_taxa_through_plots/otu_table.biom' \
1068 --output_dir summarize_taxa_through_plots_without_mapping
1069 biom convert \
1070 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L2.biom' \
1071 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L2_json.biom' \
1072 --to-json
1073 biom convert \
1074 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L3.biom' \
1075 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L3_json.biom' \
1076 --to-json
1077 biom convert \
1078 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L4.biom' \
1079 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L4_json.biom' \
1080 --to-json
1081 biom convert \
1082 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L5.biom' \
1083 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L5_json.biom' \
1084 --to-json
1085 biom convert \
1086 -i 'summarize_taxa_through_plots_without_mapping/otu_table_L6.biom' \
1087 -o 'summarize_taxa_through_plots_without_mapping/otu_table_L6_json.biom' \
1088 --to-json
1089 cp summarize_taxa_through_plots_without_mapping/*.txt test-data/summarize_taxa_through_plots/without_mapping/
1090 cp summarize_taxa_through_plots_without_mapping/*_json.biom test-data/summarize_taxa_through_plots/without_mapping/
1091 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/area_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/area_charts.html'
1092 cp summarize_taxa_through_plots_without_mapping/taxa_summary_plots/bar_charts.html 'test-data/summarize_taxa_through_plots/without_mapping/bar_charts.html'
1093
1094 # upgma_cluster
1095 upgma_cluster.py \
1096 --input_path 'test-data/upgma_cluster/' \
1097 --output_path 'test-data/upgma_cluster/'
1098
1099 # validate_mapping_file
1100 validate_mapping_file.py \
1101 -m 'test-data/validate_mapping_file/map.tsv' \
1102 -o validate_mapping_file_output \
1103 -c '_'
1104 cp validate_mapping_file_output/*.html 'test-data/validate_mapping_file/map.tsv.html'
1105 cp validate_mapping_file_output/*.log 'test-data/validate_mapping_file/map.tsv.log'
1106 cp validate_mapping_file_output/*corrected.txt 'test-data/validate_mapping_file/map.tsv_corrected.txt'
1107 rm -rf validate_mapping_file_output
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
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1126