Modularize everything and refactor gtf
This commit is contained in:
@@ -57,16 +57,9 @@
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# @option -y | --yes | --auto Assume yes answer to all questions (non-interactive mode)
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# @option -d | --debug Turn on extra debugging output
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# @option -h | --help Print help message and exit (overrides other options)
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DEBUG=1 # Turn debugging ON by default during development
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shopt -s extglob
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# @section Libraries
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# @description Change these variables to use different libraries
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JAVA="${JAVA:-java}"
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PYTHON="${PYTHON:-python3}"
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PERL="${PERL:-perl}"
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RSCRIPT="${RSCRIPT:-"R_LIBS_USER=~/R/qhtcp-workflow Rscript"}"
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DEBUG=1 # Turn debugging ON by default during development
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# @section Help
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# @description Print a helpful message
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@@ -138,7 +131,7 @@ print_help() {
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# @description Creates array and switches from user input
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# parse_input() takes all of the arguments passed to the script
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parse_input() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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long_opts="project:,module:,nomodule:,markdown,yes,auto,debug,help"
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short_opts="+p:m:n:ydh"
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@@ -267,7 +260,7 @@ random_words() {
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# @description Backup one or more files to an incremented .bk file
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# @exitcode backup iterator max 255
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backup() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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for f in "$@"; do
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[[ -e $f ]] || continue
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count=1
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@@ -428,7 +421,7 @@ module install_dependencies
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# * install.packages(c('ontologyIndex', 'ggrepel', 'tidyverse', 'sos', 'openxlsx'), dep=TRUE)
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# @noargs
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install_dependencies() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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# Dependency arrays
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depends_rpm=(graphviz pandoc pdftk-java gd-devel perl-CPAN shdoc nano rsync coreutils)
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@@ -487,7 +480,7 @@ install_dependencies() {
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"$RSCRIPT" -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
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"$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")"
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hash matlab &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
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hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
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}
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@@ -735,11 +728,10 @@ easy() {
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# Add EASY directory to the Matlab path
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# If this does not work we can try changing the -sd argument and if that fails then pushing/popping
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debug "Adding EASY directory to the Matlab path"
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hash matlab &>/dev/null &&
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matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
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"$MATLAB" -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
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# Launch matlab
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# matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
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matlab -nosplash -r "run $script"
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"$MATLAB" -nosplash -r "run $script"
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fi
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}
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@@ -757,7 +749,7 @@ ezview() {
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# Make EZview dirs
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# Start EZview
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matlab -nosplash -r "run $script"
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"$MATLAB" -nosplash -r "run $script"
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fi
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}
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@@ -962,7 +954,7 @@ module remc
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# * This allows us to abstract the program away in script-run-workflow and treat it like a module
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# @arg $1 string studyInfo file
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remc() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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# If any submodules fail the rest will not run, this is fundamental to module design
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# Remove leading && to run regardless
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@@ -993,37 +985,58 @@ remc() {
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module gtf
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# @section GTF
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# @description GTF module for QHTCP
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# @arg $1 string output directory
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# @arg $2 string gene_association.sgd
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# @arg $3 string gene_ontology_edit.obo
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# @arg $4 string ORF_List_Without_DAmPs.txt
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gtf() {
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debug "Running: ${FUNCNAME[0]}"
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process_dir="$QHTCP_PROJECT_DIR/out/gtf/process"
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function_dir="$QHTCP_PROJECT_DIR/out/gtf/function"
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component_dir="$QHTCP_PROJECT_DIR/out/gtf/component"
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out_dir="$QHTCP_PROJECT_DIR/out/gtf"
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gtf_out_dir="${1:-$QHTCP_PROJECT_DIR/out/gtf}"
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process_dir="$gtf_out_dir/process"
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function_dir="$gtf_out_dir/function"
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component_dir="$gtf_out_dir/component"
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gene_association_sgd="${2:-"$APPS_DIR/perl/gene_association.sgd"}"
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gene_ontology_obo="${3:-"$APPS_DIR/perl/gene_ontology_edit.obo"}"
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orf_list="${4:-"$APPS_DIR/perl/ORF_List_Without_DAmPs.txt"}"
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py_gtf_dcon \
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"$process_dir" \
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"$out_dir"
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"$gtf_out_dir"
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# Perform operations on each directory in parallel
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# Reproduce the function and components dirs from the process dir
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for d in "$function_dir" "$component_dir"; do
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debug "rsync -a $process_dir/ $d/"
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rsync -a "$process_dir/" "$d/"
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done
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for d in "$process_dir" "$function_dir" "$component_dir"; do
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out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
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pl_gtf "$d" "$out_dir" & # parallelize
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py_gtf_concat "$d" "$out_dir" "$out_file"
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shopt -s nullglob
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txts=("$d"/*.txt) # glob all txt files from each dir
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shopt -u nullglob
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for txt in "${txts[@]}"; do
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debug "pl_gtf_analyze -an $gene_association_sgd -as P -o $gene_ontology_obo -b $orf_list $txt"
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pl_gtf_analyze \
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'-an' "$gene_association_sgd" \
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'-as' 'P' \
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'-o' "$gene_ontology_obo" \
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'-b' "$orf_list" \
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"$txt"
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debug "pl_terms2tsv $txt"
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pl_gtf_terms2tsv "$txt"
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done
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debug "py_gtf_concat $gtf_out_dir $out_file"
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py_gtf_concat "$gtf_out_dir" "$out_file"
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done
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r_compile_gtf "$out_dir"
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r_compile_gtf "$gtf_out_dir"
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}
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module gta
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# @section GTA
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# @description GTA module for QHTCP
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# NOTES
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# * Heavily modified GTAtemplate.R
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# TODO
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# *
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# *
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@@ -1076,7 +1089,12 @@ gta() {
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zscores_file="$QHTCP_PROJECT_DIR/Exp$s/$zscores_file"
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if [[ -f $zscores_file ]]; then
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mkdir "$GTA_OUT_DIR/Exp$s"
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r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$GTA_OUT_DIR"
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r_gta \
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"Exp$s" \
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"$zscores_file" \
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"$sgd_terms_tfile" \
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"$sgd_features_file" \
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"$GTA_OUT_DIR"
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fi
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done
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@@ -1117,6 +1135,7 @@ submodule r_gta
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# @description GTAtemplate R script
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# TODO:
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# * Is GTAtemplate.R actually a template?
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# * Do we need to allow user customization?
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#
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# Files:
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# * gene_association.sgd: https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
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@@ -1136,17 +1155,20 @@ submodule r_gta
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# @arg $5 string output directory
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#
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r_gta() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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cat <<-EOF
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EOF
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script="$APPS_DIR/r/GTAtemplate.R"
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[[ -d $5 ]] || mkdir -p "$5"
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debug "$RSCRIPT $script $*"
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"$RSCRIPT" "$script" "$@"
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"$RSCRIPT" "$script" \
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"$1" \
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"$2" \
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"$3" \
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"$4" \
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"$5" \
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"${@:6}"
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}
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@@ -1216,15 +1238,13 @@ submodule r_gta_heatmaps
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# @arg $7 string output directory
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#
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r_gta_heatmaps() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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cat <<-EOF
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EOF
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script="$APPS_DIR/r/TSHeatmaps5dev2.R"
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[[ -d $5 ]] || mkdir -p "$5"
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[[ -d $7 ]] || mkdir -p "$7"
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debug "$RSCRIPT $script $*"
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"$RSCRIPT" "$script" "$@"
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}
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@@ -1265,7 +1285,7 @@ r_gta_heatmaps() {
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# script="ExpFrontend.m"
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# if ! ((YES)) &&
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# ask "Start MATLAB to run $script? This requires a GUI."; then
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# matlab -nosplash -r "$script"
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# $MATLAB -nosplash -r "$script"
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# fi
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# }
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@@ -1292,7 +1312,9 @@ r_interactions() {
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script="$APPS_DIR/r/interactions.R"
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debug "$RSCRIPT $script" "$@"
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"$RSCRIPT" "$script" "$@"
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"$RSCRIPT" "$script" \
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"$1" \
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"${@:2}" # optional arguments
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}
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@@ -1302,10 +1324,14 @@ submodule r_join_interactions
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# @arg $2 string The sd value
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# @arg $3 string The studyInfo file
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r_join_interactions() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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script="$APPS_DIR/r/joinInteractExps.R"
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debug "$RSCRIPT $script $*"
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"$RSCRIPT" "$script" "$@"
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"$RSCRIPT" "$script" \
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"$1" \
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"$2" \
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"$3" \
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"${@:4}" # optional arguments
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local out_files=("$1/REMcRdy_lm_only.csv" "$1/Shift_only.csv" "$1/parameters.csv")
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for f in "${out_files[@]}"; do
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[[ -f $f ]] || (echo "$f does not exist"; return 1)
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@@ -1314,15 +1340,18 @@ r_join_interactions() {
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submodule java_extract
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# @description Jingyu's REMc java utility using file input file REMcRdy_lm_only.csv
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# and output REMcRdy_lm_only.csv-finalTable.csv
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# I'm not sure if the output dir is configurable so we can copy data around or push/pop
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# @description Jingyu's REMc java utility
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# Input file:
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# * REMcRdy_lm_only.csv
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# Output file:
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# * REMcRdy_lm_only.csv-finalTable.csv
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# NOTE:
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# * Closed-source w/ hardcoded output directory, so have to pushd/popd to run (not ideal)
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# @arg $1 string The output directory
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java_extract() {
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debug "Running: ${FUNCNAME[0]}"
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classpath="$APPS_DIR/java/javaExtract.jar"
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out_file="$1/REMcRdy_lm_only.csv-finalTable.csv"
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# backup REMcRdy_lm_only.csv-finalTable.csv
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if ! backup "$out_file"; then
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ask "Backup of $out_file failed, continue?" || return 1
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@@ -1337,7 +1366,7 @@ java_extract() {
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debug "pushd && ${java_cmd[*]} && popd"
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pushd "$1" && "${java_cmd[@]}" && popd || return 1
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out_file="$1/REMcRdy_lm_only.csv-finalTable.csv"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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@@ -1345,17 +1374,22 @@ java_extract() {
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submodule r_add_shift_values
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# @description Add shift values back to REMcRdy_lm_only.csv-finalTable.csv
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# and output "REMcWithShift.csv" for use with the REMc heat maps
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# @arg $1 string The output csv file REMcRdy_lm_only.csv-finalTable.csv
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# @arg $1 string REMcRdy_lm_only.csv-finalTable.csv
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# @arg $2 string Shift_only.csv
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# @arg $3 string REMcWithShift.csv
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# @arg $3 string StudyInfo.csv file
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# @arg $4 string The sd value
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r_add_shift_values() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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script="$APPS_DIR/r/addShiftVals.R"
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out_file="$QHTCP_PROJECT_DIR/REMcWithShift.csv"
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debug "$RSCRIPT $script $*"
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"$RSCRIPT" "$script" "$@"
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rm -f "REMcHeatmaps/"*.pdf
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"$RSCRIPT" "$script" \
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"$1" \
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"$2" \
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"$3" \
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"$4" \
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"${@:5}" # optional arguments
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rm -f "$QHTCP_PROJECT_DIR/REMcHeatmaps/"*.pdf
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out_file="$QHTCP_PROJECT_DIR/REMcWithShift.csv"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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@@ -1365,92 +1399,87 @@ submodule r_create_heat_maps
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# @arg $1 string The final shift table (REMcWithShift.csv)
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# @arg $2 string The output directory
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r_create_heat_maps() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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script="$APPS_DIR/r/createHeatMaps.R"
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out_file="$QHTCP_PROJECT_DIR/compiledREMcHeatmaps.pdf"
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debug "$RSCRIPT $script $*"
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"$RSCRIPT" "$script" "$@"
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"$RSCRIPT" "$script" \
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"$1" \
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"$2" \
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"${@:3}" # optional arguments
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pdfs=(REMcHeatmaps/*.pdf)
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debug "pdftk ${pdfs[*]} output $out_file"
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pdftk "${pdfs[@]}" output "$out_file"
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out_file="$2/compiledREMcHeatmaps.pdf"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule r_heat_maps_homology
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# @description Execute createHeatMapsAll.R
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# @arg $1 string The final shift table (REMcRdy_lm_only.csv-finalTable.csv)
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# @arg $2 string The (Shift_only.csv)
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# @arg $1 string REMcRdy_lm_only.csv-finalTable.csv
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# @arg $2 string Shift_only.csv
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# @arg $3 string The (Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv)
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# @arg $4 string The output directory
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r_heat_maps_homology() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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script="$APPS_DIR/r/createHeatMapsHomology.R"
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out_file="$4/compiledREMcHomologyHeatmaps.pdf"
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# Clean old output
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# Remove old output
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debug "Removing old pdfs and csvs from $4"
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rm "$4/"*.{pdf,csv}
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"$RSCRIPT" "$script" \
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REMcWithShift.csv \
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Homology \
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"$APPS_DIR/r/170503_DAmPs_Only.txt" \
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Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
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"$1" \
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"$2" \
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"$3" \
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"$4" \
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"${@:5}" # optional arguments
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pdfs=("$work_dir"/homology/*.pdf)
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pdftk "${pdfs[@]}" output "$out_file"
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out_file="$4/compiledREMcHomologyHeatmaps.pdf"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule py_gtf_dcon
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# @description Perform python dcon portion of GTF
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# Output file:
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# * 1-0-0-finaltable.csv
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# @arg $1 string Directory to process
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# @arg $2 string Output directory name
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py_gtf_dcon() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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debug "Running: ${FUNCNAME[0]} $*"
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script="$APPS_DIR/python/DconJG2.py"
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debug "$PYTHON $SCRIPT $1 $2/"
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"$PYTHON" "$SCRIPT" "$1" "$2/"
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debug "$PYTHON $script $1 $2/"
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"$PYTHON" "$script" \
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"$1" \
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"$2/" \
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"${@:3}" # optional arguments
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out_file="$2/1-0-0-finaltable.csv"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule pl_gtf
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# @description Perl modules for GTF
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# @arg $1 string Working directory
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# @arg $2 string Output directory name to look for txt files
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pl_gtf() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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set1="$APPS_DIR/perl/ORF_List_Without_DAmPs.txt"
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shopt -s nullglob
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set2=("$2"/*.txt) # glob them all
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shopt -u nullglob
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for s2 in "${set2[@]}"; do
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||||
debug "pl_gtf_analyze $set1 $s2"
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pl_gtf_analyze "$set1" "$s2"
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debug "pl_terms2tsv $s2"
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pl_gtf_terms2tsv "$s2"
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||||
done
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||||
}
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||||
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||||
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||||
submodule pl_gtf_analyze
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# @description Perl analyze submodule
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# This seems weird to me because we're just overwriting the same data for all set2 members
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||||
# https://metacpan.org/dist/GO-TermFinder/view/examples/analyze.pl
|
||||
# Is there a reason you need a custom version and not the original from cpan?
|
||||
# @arg $1 string Set 1 TODO naming
|
||||
# @arg $2 string Set 2 TODO naming
|
||||
# @arg $1 string gene_association.sgd
|
||||
# @arg $2 string gene_ontology_edit.obo
|
||||
# @arg $3 string ORF_List_Without_DAmPs.txt
|
||||
# @arg $4 string TODO txt to anaylze? I'm not sure what this is called
|
||||
pl_gtf_analyze() {
|
||||
debug "Running: ${FUNCNAME[0]}"
|
||||
debug "Running: ${FUNCNAME[0]} $*"
|
||||
script="$APPS_DIR/perl/analyze_v2.pl"
|
||||
an="$APPS_DIR/perl/gene_association.sgd"
|
||||
obo="$APPS_DIR/perl/gene_ontology_edit.obo"
|
||||
debug "$PERL $script -an $an -as P -o $obo -b $1 $2"
|
||||
"$PERL" "$script" -an "$an" -as P -o "$obo" -b "$1" "$2"
|
||||
debug "$PERL $script $*"
|
||||
"$PERL" "$script" \
|
||||
"$1" \
|
||||
"$2" \
|
||||
"$3" \
|
||||
"$4" \
|
||||
"${@:5}" # optional arguments
|
||||
}
|
||||
|
||||
|
||||
@@ -1460,7 +1489,7 @@ submodule pl_gtf_terms2tsv
|
||||
#
|
||||
# @arg $1 string Terms file TODO naming
|
||||
pl_gtf_terms2tsv() {
|
||||
debug "Running: ${FUNCNAME[0]}" "$@"
|
||||
debug "Running: ${FUNCNAME[0]} $*"
|
||||
script="$APPS_DIR/perl/terms2tsv.pl"
|
||||
debug "$PERL $script $1.terms > $1.tsv"
|
||||
"$PERL" "$script" "$1.terms" > "$1.tsv"
|
||||
@@ -1471,15 +1500,14 @@ submodule py_gtf_concat
|
||||
# @description Python concat submodule for GTF
|
||||
# Concat the process ontology outputs from the /REMcReady_lm_only folder
|
||||
# Probably should be translated to bash
|
||||
# @arg $1 string working directory
|
||||
# @arg $2 string output directory name to look for txt files
|
||||
# @arg $3 string output file
|
||||
# @arg $1 string output directory name to look for txt files
|
||||
# @arg $2 string output file
|
||||
py_gtf_concat() {
|
||||
debug "Running: ${FUNCNAME[0]}"
|
||||
debug "Running: ${FUNCNAME[0]} $*"
|
||||
script="$APPS_DIR/python/concatGTFResults.py"
|
||||
debug "$PYTHON $script $2/ $3"
|
||||
"$PYTHON" "$script" "$2/" "$3"
|
||||
[[ -f $3 ]] || (echo "$3 does not exist"; return 1)
|
||||
debug "$PYTHON $script $1/ $2"
|
||||
"$PYTHON" "$script" "$1/" "$2"
|
||||
[[ -f $2 ]] || (echo "$2 does not exist"; return 1)
|
||||
}
|
||||
|
||||
|
||||
@@ -1487,7 +1515,7 @@ submodule r_compile_gtf
|
||||
# @description Compile GTF in R
|
||||
# @arg $1 string gtf output directory
|
||||
r_compile_gtf() {
|
||||
debug "Running: ${FUNCNAME[0]}"
|
||||
debug "Running: ${FUNCNAME[0]} $*"
|
||||
script="$APPS_DIR/r/CompileGTF.R"
|
||||
debug "$RSCRIPT $script $1"
|
||||
"$RSCRIPT" "$script" "$1"
|
||||
@@ -1599,9 +1627,21 @@ documentation() {
|
||||
# Most variables in main() are user configurable or can be overriden by env
|
||||
# @internal
|
||||
main() {
|
||||
debug "Running: ${FUNCNAME[0]}" "$@"
|
||||
|
||||
# Some global vars
|
||||
debug "Running: ${FUNCNAME[0]} $*"
|
||||
|
||||
# Libraries
|
||||
declare -g JAVA="${JAVA:-$(which java 2>/dev/null)}"
|
||||
declare -g PYTHON="${PYTHON:-$(which python3 2>/dev/null)}"
|
||||
declare -g PERL="${PERL:-$(which perl 2>/dev/null)}"
|
||||
declare -g RSCRIPT="${RSCRIPT:-$(which Rscript 2>/dev/null)}"
|
||||
declare -g MATLAB="${MATLAB:-$(which matlab 2>/dev/null)}"
|
||||
|
||||
# Use a custom R library
|
||||
declare -gx R_LIBS_USER="$HOME/R/$SCRIPT_NAME"
|
||||
[[ -d "$R_LIBS_USER" ]] || mkdir -p "$R_LIBS_USER"
|
||||
|
||||
# Global vars
|
||||
SCRIPT_NAME="${BASH_SOURCE[0]}"
|
||||
SCRIPT=$(realpath -s "${BASH_SOURCE[0]}")
|
||||
SCRIPT_DIR=$(dirname "$SCRIPT")
|
||||
APPS_DIR="$SCRIPT_DIR/apps"
|
||||
@@ -1610,13 +1650,18 @@ main() {
|
||||
DATE="$(date +%Y%m%d)" # change in EASYconsole.m to match 'hardcode'
|
||||
|
||||
# Find a scans directory
|
||||
# TODO change back for production, avoid actual scan dirs during testing
|
||||
# local scans_heirarchy=("./scans" "/mnt/data/scans" "/mnt/data/ExpJobs" "./scans")
|
||||
local scans_heirarchy=( "$SCANS_DIR" "$SCRIPT_DIR/scans" "/mnt/data/scans" "templates/scans-demo" "./scans")
|
||||
local scans_heirarchy=(
|
||||
"$SCANS_DIR"
|
||||
"$SCRIPT_DIR/scans"
|
||||
"/mnt/data/scans"
|
||||
"$SCRIPT_DIR/templates/scans-demo"
|
||||
"$SCRIPT_DIR/scans" # fallback and create if others not found
|
||||
)
|
||||
|
||||
[[ -z $SCANS_DIR ]] && for d in "${scans_heirarchy[@]}"; do
|
||||
if [[ -d $d ]]; then
|
||||
declare -g SCANS_DIR="$d"
|
||||
declare -gx SCANS_DIR="$d"
|
||||
fi
|
||||
done
|
||||
if ! [[ -d $SCANS_DIR ]]; then
|
||||
@@ -1644,7 +1689,8 @@ main() {
|
||||
|
||||
if [[ -z $OUT_DIR ]]; then
|
||||
echo "No output directory found"
|
||||
declare -g OUT_DIR="$SCRIPT_DIR/out"
|
||||
declare -gx OUT_DIR="$SCRIPT_DIR/out"
|
||||
# This is not something we do often, so ask
|
||||
if ask "Create $SCRIPT_DIR/out?"; then
|
||||
debug "mkdir $SCRIPT_DIR/out"
|
||||
mkdir "$SCRIPT_DIR/out"
|
||||
|
||||
Reference in New Issue
Block a user