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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
Upload preparations done for BioLinux to Debian

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examples/qiime_tutorial/qiime_tutorial_commands_serial.sh
 
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#!/bin/bash
 
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# interactive commands are commented out
 
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#print_qiime_config.py
 
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# Pre-processing
 
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echo "Check mapping file"
 
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rm -rf mapping_output ; check_id_map.py -m Fasting_Map.txt -o mapping_output -v
 
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echo "Demultiplexing"
 
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rm -rf split_library_output ; split_libraries.py -m Fasting_Map.txt -f Fasting_Example.fna -q Fasting_Example.qual -o split_library_output
 
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# otus
 
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echo "Pick OTUs through OTU table"
 
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rm -rf otus ; pick_de_novo_otus.py -i split_library_output/seqs.fna -o otus
 
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#print_biom_table_summary.py -i otus/otu_table.biom
 
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#OTU Heatmap
 
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echo "OTU Heatmap"
 
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make_otu_heatmap_html.py -i otus/otu_table.biom -o otus/OTU_Heatmap/
 
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#OTU Network
 
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echo "OTU Network"
 
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make_otu_network.py -m Fasting_Map.txt -i otus/otu_table.biom -o otus/OTU_Network
 
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#Make Taxa Summary Charts
 
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echo "Summarize taxa"
 
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rm -rf wf_taxa_summary ; summarize_taxa_through_plots.py -i otus/otu_table.biom -o wf_taxa_summary -m Fasting_Map.txt
 
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echo "Alpha rarefaction"
 
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#alpha_diversity.py -h
 
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echo "alpha_diversity:metrics shannon,PD_whole_tree,chao1,observed_species" > alpha_params.txt
 
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rm -rf wf_arare ; alpha_rarefaction.py -i otus/otu_table.biom -m Fasting_Map.txt -o wf_arare/ -p alpha_params.txt -t otus/rep_set.tre
 
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echo "Beta diversity and plots"
 
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rm -rf wf_bdiv_even146 ; beta_diversity_through_plots.py -i otus/otu_table.biom -m Fasting_Map.txt -o wf_bdiv_even146/ -t otus/rep_set.tre -e 146
 
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echo "Jackknifed beta diversity"
 
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rm -rf wf_jack ; jackknifed_beta_diversity.py -i otus/otu_table.biom -t otus/rep_set.tre -m Fasting_Map.txt -o wf_jack -e 110
 
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echo "Make Bootstrapped Tree"
 
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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
 
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echo "Make Bi-Plots"
 
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rm -rf 3d_biplot ; make_3d_plots.py -i wf_bdiv_even146/unweighted_unifrac_pc.txt -m Fasting_Map.txt -t wf_taxa_summary/otu_table_L3.txt --n_taxa_keep 5 -o 3d_biplot