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organize_dir_structure_V2.sh
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organize_dir_structure_V2.sh
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#/usr/bin/env bash
#########
#Please address any bugs to Cheng.
#Date 2017.12.19
#########
mapping_file=$1
category_1=$2
SCRIPTPATH=$3
number=$4
if_picrust=$5
prefix=$6
if [ -z "$3" ]; then
echo "##########
Please prepare the directory structure before starting the program like below:
raw/fastq_files ...
mapping_file
manifest_file
\n\n"
echo "Please provide following input parameters
1) Full path of the mapping file. (Accept both .csv or txt format.)
2) The name of the first category in the mapping file.
Sample Usage:
sh $0 M231_Mapping_2.tsv Group1 readme.pdf
"
exit 0
else
echo "################
Running: sh $0 $1 $2 $3 $4 $5 $6"
fi
check_file() {
echo "Checking file for $1 ..."
file_name=$1
if [ -f $file_name ]; then
echo "File $file_name exists"
else
echo "File $file_name does not exist"
exit
fi
}
echo "##############################################################\n#Organize the Result folder"
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
if [ -d "./Result" ];then
rm -r ./Result;
fi;
mkdir -p ./Result/ \
./Result/2-AbundanceAnalysis/ ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/ \
./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/ \
./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/3-CollapsedStats/ \
./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/ \
./Result/2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/ \
./Result/2-AbundanceAnalysis/2-AbundanceComparison/1-ANCOM/ \
./Result/2-AbundanceAnalysis/2-AbundanceComparison/2-ANOVA/ \
./Result/2-AbundanceAnalysis/2-AbundanceComparison/3-KruskalWallis/ \
./Result/2-AbundanceAnalysis/2-AbundanceComparison/4-LEfSe/ \
./Result/2-AbundanceAnalysis/2-AbundanceComparison/5-DESeq2/ \
./Result/3-AlphaDiversity/1-AlphaDiversitySummary/ \
./Result/3-AlphaDiversity/2-AlphaRarefaction/ \
./Result/3-AlphaDiversity/3-SignificanceAnalysis/1-Wilcox_Test/ \
./Result/3-AlphaDiversity/3-SignificanceAnalysis/2-Kruskal_Wallis/ \
./Result/4-BetaDiversity/1-BetaDiversitySummary/ \
./Result/4-BetaDiversity/2-PCoA/ \
./Result/4-BetaDiversity/3-NMDS/ \
./Result/4-BetaDiversity/4-PLS-DA/ \
./Result/4-BetaDiversity/5-GroupSignificance/ \
./Result/4-BetaDiversity/6-PCA/ \
./Result/5-Phylogenetics/ \
./Result/6-AssociationAnalysis/1-RDA/ \
./Result/FiguresTablesForReport \
./Result/4-BetaDiversity/2-PCoA/PCoA-Phyloseq \
./Result/4-BetaDiversity/2-PCoA/PCoA-Qiime2
if [[ $if_picrust == 'yes' ]]; then
mkdir mkdir -p ./Result/7-FunctionAnalysis/1-KEGG_Pathway/ \
./Result/7-FunctionAnalysis/2-PCAPlots/ \
./Result/7-FunctionAnalysis/3-SignifcanceAnalysis/ \
./Result/7-FunctionAnalysis/3-SignifcanceAnalysis/1-DunnTest
fi
echo "Start organize the files for deliverables ..."
cp ${SCRIPTPATH}/Result_README.pdf ./Result/
cp $mapping_file ./Result/mapping_file.txt
cp ${category_1}_classified_stat_relative.xls ${category_1}_classified_stat_relative.png ./Result/2-AbundanceAnalysis/
cp exported/Absolute/*absolute.txt ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/
#cp exported/Absolute/otu_table.p.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Phylum.absolute.txt
#cp exported/Absolute/otu_table.c.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Class.absolute.txt
#cp exported/Absolute/otu_table.o.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Order.absolute.txt
#cp exported/Absolute/otu_table.f.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Family.absolute.txt
#cp exported/Absolute/otu_table.g.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Genus.absolute.txt
#cp exported/Absolute/otu_table.s.absolute.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/1-Absolute/feature-table.Species.absolute.txt
cp exported/Relative/*relative.txt ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/
#cp exported/Relative/otu_table.p.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Phylum.relative.txt
#cp exported/Relative/otu_table.c.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Class.relative.txt
#cp exported/Relative/otu_table.o.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Order.relative.txt
#cp exported/Relative/otu_table.f.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Family.relative.txt
#cp exported/Relative/otu_table.g.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Genus.relative.txt
#cp exported/Relative/otu_table.s.relative.mat ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/2-Relative/feature-table.Species.relative.txt
cp -r exported/collapsed/*qzv* ./Result/2-AbundanceAnalysis/1-AbundanceSummary/1-AbundanceTable/3-CollapsedStats/
cp -r taxa-bar-plots.qzv* ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/
#cp -r exported/Relative/*relative.txt exported/Relative/otu*png ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots-top20
# cp -r exported/${number}/*.qzv* ./Result/2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/Heatmap-Qiime2/
cp -r Heatmap_top20 ./Result/2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/
cp -r Heatmap_top20_clustered ./Result/2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/
cp -r exported/ANCOM/*.qzv* ./Result/2-AbundanceAnalysis/2-AbundanceComparison/1-ANCOM/
cp TaxaStatistic/* ./Result/2-AbundanceAnalysis/
cp -r exported/DiffAbundance/ANOVA_*txt ./Result/2-AbundanceAnalysis/2-AbundanceComparison/2-ANOVA/
cp -r exported/DiffAbundance/kruskal_wallis_*txt ./Result/2-AbundanceAnalysis/2-AbundanceComparison/3-KruskalWallis/
#cp lefse result ./Result/2-AbundanceAnalysis/2-AbundanceComparison/4-LEfSe/
cp -r exported/Relative/Lefse/*/ ./Result/2-AbundanceAnalysis/2-AbundanceComparison/4-LEfSe/
cp -r exported/DiffAbundance/DESeq2_*txt ./Result/2-AbundanceAnalysis/2-AbundanceComparison/5-DESeq2/
cp -rp tables_for_deseq_anova_kruskal ./Result/2-AbundanceAnalysis/2-AbundanceComparison/
cp -r alpha/alpha-summary.tsv R_output/*alpha_diversity_* ./Result/3-AlphaDiversity/1-AlphaDiversitySummary/
cp -r alpha-rarefaction.qzv* ./Result/3-AlphaDiversity/2-AlphaRarefaction/
cp -r alpha/*wilcox* ./Result/3-AlphaDiversity/3-SignificanceAnalysis/1-Wilcox_Test/
#cp -r core-metrics-results/observed*qzv* ./Result/3-AlphaDiversity/3-SignificanceAnalysis/2-Kruskal_Wallis/
#cp -r core-metrics-results/shannon*qzv* ./Result/3-AlphaDiversity/3-SignificanceAnalysis/2-Kruskal_Wallis/
#cp -r core-metrics-results/faith*qzv* ./Result/3-AlphaDiversity/3-SignificanceAnalysis/2-Kruskal_Wallis/
cp -r alpha_groupsignificance/* ./Result/3-AlphaDiversity/3-SignificanceAnalysis/2-Kruskal_Wallis/
cp -r R_output/*matrix.xls R_output/BetaDiversity_heatmap.png ./Result/4-BetaDiversity/1-BetaDiversitySummary/
cp -r R_output/*summary.pdf ./Result/4-BetaDiversity/1-BetaDiversitySummary/
cp -r core-metrics-results/*_emperor.qzv* ./Result/4-BetaDiversity/2-PCoA/PCoA-Qiime2
cp -r R_output/*PCoA* ./Result/4-BetaDiversity/2-PCoA/PCoA-Phyloseq
cp -r R_output/*NMDS* ./Result/4-BetaDiversity/3-NMDS/
cp -r core-metrics-results/*permanova*significance.qzv* ./Result/4-BetaDiversity/5-GroupSignificance/
cp -r core-metrics-results/*anosim*significance.qzv* ./Result/4-BetaDiversity/5-GroupSignificance/
#cp -r R_output/unifrac*summary.pdf ./Result/4-BetaDiversity/1-BetaDiversitySummary/
#cp -r core-metrics-results/unweighted*_emperor.qzv* R_output/*unifrac*PCoA* ./Result/4-BetaDiversity/2-PCoA/
#cp -r R_output/*unifrac*NMDS* ./Result/4-BetaDiversity/3-NMDS/
#cp -r core-metrics-results/unweighted*significance.qzv* ./Result/4-BetaDiversity/5-GroupSignificance/
#cp -r R_output/wunifrac*summary.pdf ./Result/4-BetaDiversity/1-BetaDiversitySummary/
#cp -r core-metrics-results/weighted*_emperor.qzv* R_output/*wunifrac*PCoA* ./Result/4-BetaDiversity/2-PCoA/
#cp -r R_output/*wunifrac*NMDS* ./Result/4-BetaDiversity/3-NMDS/
cp -r R_output/*PLSDA* ./Result/4-BetaDiversity/4-PLS-DA/
cp -r R_output/*PCA* ./Result/4-BetaDiversity/6-PCA/
#cp -r core-metrics-results/weighted*significance.qzv* ./Result/4-BetaDiversity/5-GroupSignificance/
cp -r exported/feature-table.taxonomy.txt ./Result/2-AbundanceAnalysis/${category_1}_feature-table.taxonomy.txt
cp dna-sequences.fasta ./Result/5-Phylogenetics/${category_1}_representative-sequence.fasta
cp tree.nwk ./Result/5-Phylogenetics/${category_1}_rooted-tree.nwk
#cp -r R_output/Bacteria.phylogeny.pdf ./Result/5-Phylogenetics/1-MajorPhylums/
#cp -r phylogeny/tol_* phylogeny/tree.rooted.nwk ./Result/5-Phylogenetics/2-MajorOTUs/
#cp -r phylogeny/tol_* phylogeny/tree.rooted.nwk ./Result/5-Phylogenetics/
cp -r exported/Absolute/RDA/* ./Result/6-AssociationAnalysis/1-RDA/
#rm ./Result/6-AssociationAnalysis/1-RDA/*/data.txt ./Result/6-AssociationAnalysis/1-RDA/*/rda.R
#cp -r exported/Absolute/p.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Phylum.rda.pdf
#cp -r exported/Absolute/c.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Class.rda.pdf
#cp -r exported/Absolute/o.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Order.rda.pdf
#cp -r exported/Absolute/f.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Family.rda.pdf
#cp -r exported/Absolute/g.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Genus.rda.pdf
#cp -r exported/Absolute/s.rda.pdf ./Result/6-AssociationAnalysis/1-RDA/Species.rda.pdf
#cp -r /Result/6-AssociationAnalysis
if [[ $if_picrust == 'yes' ]]; then
cp -rp 2-ANOVA_And_Duncan/ ./Result/7-FunctionAnalysis/3-SignifcanceAnalysis/
cp -r closedRef_forPICRUSt/feature-table.metagenome.L1.txt closedRef_forPICRUSt/feature-table.metagenome.L2.txt closedRef_forPICRUSt/feature-table.metagenome.L3.txt ./Result/7-FunctionAnalysis/1-KEGG_Pathway/
#rm ./Result/7-FunctionAnalysis/1-KEGG_Pathway/*PCA* ./Result/7-FunctionAnalysis/1-KEGG_Pathway/*DunnTest*
cp -rp closedRef_forPICRUSt/function-bar-plots-top20-group-mean closedRef_forPICRUSt/function-bar-plots-top20 ./Result/7-FunctionAnalysis/1-KEGG_Pathway/
cp -r closedRef_forPICRUSt/*PCA*pdf ./Result/7-FunctionAnalysis/2-PCAPlots/
cp -r closedRef_forPICRUSt/*DunnTest*xls ./Result/7-FunctionAnalysis/3-SignifcanceAnalysis/1-DunnTest/
fi
#mv ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L1.PCA.txt.PCA.pdf ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L1.PCA.pdf
#mv ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L2.PCA.txt.PCA.pdf ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L2.PCA.pdf
#mv ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L3.PCA.txt.PCA.pdf ./Result/7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L3.PCA.pdf
#rm ./Result/7-FunctionAnalysis/2-PCAPlots/PCA*/PCA.R ./Result/7-FunctionAnalysis/2-PCAPlots/PCA*/Rplots.pdf
cp AdditionalPhylogeny/*.pdf AdditionalPhylogeny/*table.xls ./Result/5-Phylogenetics/
cp -rp 4-VennAndFlower/ ./Result/1-VennAndFlower
rm ./Result/1-VennAndFlower/*.log
cp -rp 3-NetworkAnalysis/ ./Result/6-AssociationAnalysis/
cp -rp 2-CorrelationHeatmap/ ./Result/6-AssociationAnalysis/
cp -rp alpha-rarefaction-ggplot2/ ./Result/3-AlphaDiversity/2-AlphaRarefaction/
cp -rp Barplot-of-Group-Mean/ ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots-top20-group-mean
cp -rp taxa-bar-plots-top20-group-ordered/ ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots-top20
#rm ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots-top20-group-mean/*svg
#change index.html to a more obvious name, and organize the qzv.exported and qzv files.
#cd ./Result/
for f in $(find ./Result/ -type f -name "*qzv"); do echo $f; base=$(basename $f .qzv); dir=$(dirname $f); mv $f ${f}.exported; mv ${f}.exported ${dir}/${base}; done
for f in $(find ./Result/ -type f -name "index.html") ; do echo $f; base=$(basename $f .html); dir=$(dirname $f); new=${dir}/Summary_请点此文件查看.html; mv $f $new; done
#cd ../
#minor adjustment of file structure
mv ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots/ ./Result/2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots_Qiime2
mv ./Result/3-AlphaDiversity/2-AlphaRarefaction/alpha-rarefaction ./Result/3-AlphaDiversity/2-AlphaRarefaction/alpha-rarefaction-Qiime2
rm -r ./Result/4-BetaDiversity/2-PCoA/PCoA-Qiime2/jaccard_emperor
###rename the pcoa results
#mv ./Result/4-BetaDiversity/*emperor* ./Result/4-BetaDiversity/2-PCoA/1-Plots-from-QIIME2
#mv ./Result/4-BetaDiversity/*PCoA* ./Result/4-BetaDiversity/2-PCoA/2-Plots-from-R
#######################For FiguresTablesForReport
cp -rp ${SCRIPTPATH}/Report/src Result/FiguresTablesForReport/
cp ${SCRIPTPATH}/Report/结题报告.html Result/
cd ./Result/FiguresTablesForReport
#cp -rp ../2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/Heatmap-Qiime2/${category_1}-table-Phylum.${number}/ page4
cp ../2-AbundanceAnalysis/1-AbundanceSummary/3-Heatmaps/Heatmap_top20_clustered/Phylum/heatmap.pdf Figure4-3.pdf
cp -rp ../2-AbundanceAnalysis/2-AbundanceComparison/1-ANCOM/${category_1}.ANCOM.Genus/ page4-2
cp -rp ../4-BetaDiversity/5-GroupSignificance/unweighted_unifrac-permanova-${category_1}-significance/ page6-2
#cp ../1-QCStats/1-Stats-demux/demultiplex-summary.png Figure3-1.png
#cp ../2-AbundanceAnalysis/Classified_stat_relative.png Figure4-1.png
cp ../2-AbundanceAnalysis/1-AbundanceSummary/2-Barplots/taxa-bar-plots-top20-group-mean/${category_1}_Phylum_mean_barplot.pdf Figure4-2.pdf
cp ../2-AbundanceAnalysis/2-AbundanceComparison/4-LEfSe/Genus/${category_1}_Genus_lefse_LDA2.pdf Figure4-4.pdf
cp ../2-AbundanceAnalysis/2-AbundanceComparison/4-LEfSe/Genus/${category_1}_Genus_lefse_LDA2.cladogram.pdf Figure4-5.pdf
cp ../1-VennAndFlower/${category_1}_Venn_plot.png Figure4-6.png
cp ../3-AlphaDiversity/1-AlphaDiversitySummary/${category_1}_alpha_diversity_shannon.boxplot.pdf Figure5-1.pdf
cp ../3-AlphaDiversity/3-SignificanceAnalysis/1-Wilcox_Test/shannon_${category_1}_wilcox_compare_boxplot.png Figure5-2.png
cp ../4-BetaDiversity/1-BetaDiversitySummary/BetaDiversity_heatmap.png Figure6-1.png
cp ../4-BetaDiversity/3-NMDS/${category_1}_unweighted_unifrac_NMDS_without_labels.pdf Figure6-2.pdf
cp ../5-Phylogenetics/${category_1}_phylogenetic_tree_heatmap.pdf Figure7-1.pdf
cp ../6-AssociationAnalysis/1-RDA/Genus/${prefix}${category_1}*features_location_plot.pdf Figure8-1.pdf
cp ../6-AssociationAnalysis/2-CorrelationHeatmap/Genus/${prefix}Correlation_heatmap.pdf Figure8-2.pdf
cp ../6-AssociationAnalysis/3-NetworkAnalysis/Genus/Correlation_network.pdf Figure8-3.pdf
if [[ $if_picrust == 'yes' ]]; then
cp ../7-FunctionAnalysis/1-KEGG_Pathway/function-bar-plots-top20-group-mean/${category_1}_L1_mean_*.pdf Figure9-1.pdf
cp ../7-FunctionAnalysis/2-PCAPlots/feature-table.metagenome.L1.${category_1}.PCA.pdf Figure9-2.pdf
cp ../7-FunctionAnalysis/3-SignifcanceAnalysis/2-ANOVA_And_Duncan/${category_1}_all_significant_pathway_barplot_of_duncan.pdf Figure9-3.pdf
fi
if [ -f Figure4-2.pdf ];then echo "Converting pdf to png"; for pdfs in *.pdf; do echo $pdfs; base=$(basename $pdfs .pdf); convert -density 300 -quality 80 $pdfs ${base}.png; rm $pdfs;done;fi;
python ~/github/Bayegy/convert_to_html_table.py -i ../../../Result/1-OTUStats/2-Stats-dada2/Summary_请点此文件查看.html -o src/pages/main_cleaned.html -t dada2html -k '无法加载表格表3-1'