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qiime_tutorial_commands_parallel.sh
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qiime_tutorial_commands_parallel.sh
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#!/bin/bash
# Pre-processing
echo "Check Mapping"
rm -r mapping_output ; check_id_map.py -m Fasting_Map.txt -o mapping_output
echo "De-multiplexing"
rm -r split_library_output ; split_libraries.py -m Fasting_Map.txt -f Fasting_Example.fna -q Fasting_Example.qual -o split_library_output
# Data analysis
echo "Pick OTUs through OTU table"
rm -r wf_da ; pick_otus_through_otu_table.py -i split_library_output/seqs.fna -p custom_parameters.txt -o wf_da -a
#OTU table visualization
echo "Even-sampling rarefaction"
single_rarefaction.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -d 146 -o wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/rarified_otu_table.txt
#OTU Heatmap
echo "OTU Heatmap"
make_otu_heatmap_html.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/OTU_Heatmap
#OTU Network
echo "OTU Network"
make_otu_network.py -m Fasting_Map.txt -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/OTU_Network
#Make Pie Charts
echo "Summarize taxa"
summarize_taxa.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/otu_table_Level3.txt -L 3 -r 0
echo "Make Pie Charts"
make_pie_charts.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/otu_table_Level3.txt -l Phylum -o wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/Pie_Charts -k white -s
# Alpha rarefaction
rm -r wf_arare ; alpha_rarefaction.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -m Fasting_Map.txt -o wf_arare/ -p custom_parameters.txt -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -a
# Beta diversity, 3d plots
rm -r wf_bdiv ; beta_diversity_through_3d_plots.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -m Fasting_Map.txt -o wf_bdiv/ -p custom_parameters.txt -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -a
echo "Make 2D Plots - Unweighted Unifrac"
make_2d_plots.py -i wf_bdiv/unweighted_unifrac_pc.txt -m Fasting_Map.txt -o wf_bdiv/unweighted_unifrac_2d -k white -p wf_bdiv/prefs.txt
echo "Make Distance Histograms - Unweighted Unifrac"
make_distance_histograms.py -d wf_bdiv/unweighted_unifrac_seqs_otu_table.txt -m Fasting_Map.txt -o wf_bdiv/Distance_Histograms -p wf_bdiv/prefs.txt --html_output
# Jackknifed UPGMA
rm -r wf_jack/; jackknifed_upgma.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_jack -p custom_parameters.txt -e 110 -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -a
echo "Make Bootstrapped Tree"
make_bootstrapped_tree.py -m wf_jack/unweighted_unifrac/upgma_cmp/master_tree.tre -s wf_jack/unweighted_unifrac/upgma_cmp/jackknife_support.txt -o wf_jack/unweighted_unifrac/upgma_cmp/jackknife_named_nodes.pdf
#rm -r mapping_output
#rm -r split_library_output
#rm -r wf_da
#rm -r wf_arare
#rm -r wf_bdiv
#rm -r wf_jack
#rm -r jobs