From 5ca6ef8f01ed5253f506c2c5f94e255866278e23 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Fri, 2 Aug 2024 17:52:44 -0400
Subject: [PATCH] Modularize everything and refactor gtf

---
 workflow/qhtcp-workflow | 270 +++++++++++++++++++++++-----------------
 1 file changed, 158 insertions(+), 112 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index b3c37097..b8068300 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -57,16 +57,9 @@
 # @option -y | --yes | --auto Assume yes answer to all questions (non-interactive mode)
 # @option -d | --debug Turn on extra debugging output
 # @option -h | --help Print help message and exit (overrides other options)
-
-DEBUG=1 # Turn debugging ON by default during development
 shopt -s extglob
 
-# @section Libraries
-# @description Change these variables to use different libraries
-JAVA="${JAVA:-java}"
-PYTHON="${PYTHON:-python3}"
-PERL="${PERL:-perl}"
-RSCRIPT="${RSCRIPT:-"R_LIBS_USER=~/R/qhtcp-workflow Rscript"}"
+DEBUG=1 # Turn debugging ON by default during development
 
 # @section Help
 # @description Print a helpful message
@@ -138,7 +131,7 @@ print_help() {
 # @description Creates array and switches from user input
 # parse_input() takes all of the arguments passed to the script
 parse_input() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
 
   long_opts="project:,module:,nomodule:,markdown,yes,auto,debug,help"
   short_opts="+p:m:n:ydh"
@@ -267,7 +260,7 @@ random_words() {
 # @description Backup one or more files to an incremented .bk file
 # @exitcode backup iterator max 255
 backup() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   for f in "$@"; do
     [[ -e $f ]] || continue
     count=1
@@ -428,7 +421,7 @@ module install_dependencies
 #   * install.packages(c('ontologyIndex', 'ggrepel', 'tidyverse', 'sos', 'openxlsx'), dep=TRUE)
 # @noargs
 install_dependencies() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
 
   # Dependency arrays
   depends_rpm=(graphviz pandoc pdftk-java gd-devel perl-CPAN shdoc nano rsync coreutils)
@@ -487,7 +480,7 @@ install_dependencies() {
   "$RSCRIPT" -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
   "$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")"
 
-  hash matlab &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
+  hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
 }
 
 
@@ -735,11 +728,10 @@ easy() {
     # Add EASY directory to the Matlab path
     # If this does not work we can try changing the -sd argument and if that fails then pushing/popping
     debug "Adding EASY directory to the Matlab path"
-    hash matlab &>/dev/null && 
-    matlab -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
+    "$MATLAB" -nodisplay -nosplash -nodesktop -nojvm -batch "addpath('$EASY_DIR')"
     # Launch matlab
     # matlab -nosplash -sd "$PROJECT_SCANS_DIR" -r "run $script"
-    matlab -nosplash -r "run $script"
+    "$MATLAB" -nosplash -r "run $script"
   fi
 }
 
@@ -757,7 +749,7 @@ ezview() {
     # Make EZview dirs
 
     # Start EZview
-    matlab -nosplash -r "run $script"
+    "$MATLAB" -nosplash -r "run $script"
   fi
 }
 
@@ -962,7 +954,7 @@ module remc
 #     * This allows us to abstract the program away in script-run-workflow and treat it like a module
 # @arg $1 string studyInfo file
 remc() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
 
   # If any submodules fail the rest will not run, this is fundamental to module design
   # Remove leading && to run regardless
@@ -993,37 +985,58 @@ remc() {
 module gtf
 # @section GTF
 # @description GTF module for QHTCP
+# @arg $1 string output directory
+# @arg $2 string gene_association.sgd
+# @arg $3 string gene_ontology_edit.obo
+# @arg $4 string ORF_List_Without_DAmPs.txt
 gtf() {
   debug "Running: ${FUNCNAME[0]}"
-  process_dir="$QHTCP_PROJECT_DIR/out/gtf/process"
-  function_dir="$QHTCP_PROJECT_DIR/out/gtf/function"
-  component_dir="$QHTCP_PROJECT_DIR/out/gtf/component"
-  out_dir="$QHTCP_PROJECT_DIR/out/gtf"
+  gtf_out_dir="${1:-$QHTCP_PROJECT_DIR/out/gtf}"
+  process_dir="$gtf_out_dir/process"
+  function_dir="$gtf_out_dir/function"
+  component_dir="$gtf_out_dir/component"
+
+  gene_association_sgd="${2:-"$APPS_DIR/perl/gene_association.sgd"}"
+  gene_ontology_obo="${3:-"$APPS_DIR/perl/gene_ontology_edit.obo"}"
+  orf_list="${4:-"$APPS_DIR/perl/ORF_List_Without_DAmPs.txt"}"
 
   py_gtf_dcon \
     "$process_dir" \
-    "$out_dir"
+    "$gtf_out_dir"
 
-  # Perform operations on each directory in parallel
+  # Reproduce the function and components dirs from the process dir
   for d in "$function_dir" "$component_dir"; do
     debug "rsync -a $process_dir/ $d/"
     rsync -a "$process_dir/" "$d/"
   done
+
   for d in "$process_dir" "$function_dir" "$component_dir"; do
     out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
-    pl_gtf "$d" "$out_dir" & # parallelize
-    py_gtf_concat "$d" "$out_dir" "$out_file"
+    shopt -s nullglob
+    txts=("$d"/*.txt) # glob all txt files from each dir
+    shopt -u nullglob
+    for txt in "${txts[@]}"; do
+      debug "pl_gtf_analyze -an $gene_association_sgd -as P -o $gene_ontology_obo -b $orf_list $txt"
+      pl_gtf_analyze \
+        '-an' "$gene_association_sgd" \
+        '-as' 'P' \
+        '-o' "$gene_ontology_obo" \
+        '-b' "$orf_list" \
+        "$txt"
+      debug "pl_terms2tsv $txt"
+      pl_gtf_terms2tsv "$txt"
+    done
+    debug "py_gtf_concat $gtf_out_dir $out_file"
+    py_gtf_concat "$gtf_out_dir" "$out_file"
   done
 
-  r_compile_gtf "$out_dir"
+  r_compile_gtf "$gtf_out_dir"
 }
 
 
 module gta
 # @section GTA
 # @description GTA module for QHTCP
-# NOTES
-#   * Heavily modified GTAtemplate.R
 # TODO
 #   * 
 #   * 
@@ -1076,7 +1089,12 @@ gta() {
     zscores_file="$QHTCP_PROJECT_DIR/Exp$s/$zscores_file"
     if [[ -f $zscores_file ]]; then
       mkdir "$GTA_OUT_DIR/Exp$s"
-      r_gta "Exp$s" "$zscores_file" "$sgd_terms_tfile" "$sgd_features_file" "$GTA_OUT_DIR"
+      r_gta \
+        "Exp$s" \
+        "$zscores_file" \
+        "$sgd_terms_tfile" \
+        "$sgd_features_file" \
+        "$GTA_OUT_DIR"
     fi
   done
 
@@ -1117,6 +1135,7 @@ submodule r_gta
 # @description GTAtemplate R script
 # TODO:
 #   * Is GTAtemplate.R actually a template?
+#   * Do we need to allow user customization?
 #
 # Files:
 #   * gene_association.sgd: https://downloads.yeastgenome.org/curation/chromosomal_feature/gene_association.sgd
@@ -1136,17 +1155,20 @@ submodule r_gta
 # @arg $5 string output directory
 #
 r_gta() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   cat <<-EOF
 
 	EOF
-
   script="$APPS_DIR/r/GTAtemplate.R"
-
   [[ -d $5 ]] || mkdir -p "$5"
-
   debug "$RSCRIPT $script $*"
-  "$RSCRIPT" "$script" "$@"
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "$2" \
+    "$3" \
+    "$4" \
+    "$5" \
+    "${@:6}"
 }
 
 
@@ -1216,15 +1238,13 @@ submodule r_gta_heatmaps
 # @arg $7 string output directory
 #
 r_gta_heatmaps() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   cat <<-EOF
 
 	EOF
-
   script="$APPS_DIR/r/TSHeatmaps5dev2.R"
 
-  [[ -d $5 ]] || mkdir -p "$5"
-
+  [[ -d $7 ]] || mkdir -p "$7"
   debug "$RSCRIPT $script $*"
   "$RSCRIPT" "$script" "$@"
 }
@@ -1265,7 +1285,7 @@ r_gta_heatmaps() {
 #   script="ExpFrontend.m"
 #   if ! ((YES)) && 
 #   ask "Start MATLAB to run $script? This requires a GUI."; then
-#     matlab -nosplash -r "$script"
+#     $MATLAB -nosplash -r "$script"
 #   fi
 # }
 
@@ -1292,7 +1312,9 @@ r_interactions() {
   script="$APPS_DIR/r/interactions.R"
 
   debug "$RSCRIPT $script" "$@"
-  "$RSCRIPT" "$script" "$@"
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "${@:2}" # optional arguments
 }
 
 
@@ -1302,10 +1324,14 @@ submodule r_join_interactions
 # @arg $2 string The sd value
 # @arg $3 string The studyInfo file
 r_join_interactions() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   script="$APPS_DIR/r/joinInteractExps.R"
   debug "$RSCRIPT $script $*"
-  "$RSCRIPT" "$script" "$@"
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "$2" \
+    "$3" \
+    "${@:4}" # optional arguments
   local out_files=("$1/REMcRdy_lm_only.csv" "$1/Shift_only.csv" "$1/parameters.csv")
   for f in "${out_files[@]}"; do
     [[ -f $f ]] || (echo "$f does not exist"; return 1)
@@ -1314,15 +1340,18 @@ r_join_interactions() {
 
 
 submodule java_extract
-# @description Jingyu's REMc java utility using file input file REMcRdy_lm_only.csv 
-# and output REMcRdy_lm_only.csv-finalTable.csv
-# I'm not sure if the output dir is configurable so we can copy data around or push/pop
+# @description Jingyu's REMc java utility
+# Input file:
+#   * REMcRdy_lm_only.csv 
+# Output file:
+#   * REMcRdy_lm_only.csv-finalTable.csv
+# NOTE:
+#   * Closed-source w/ hardcoded output directory, so have to pushd/popd to run (not ideal)
 # @arg $1 string The output directory
 java_extract() {
   debug "Running: ${FUNCNAME[0]}"
   classpath="$APPS_DIR/java/javaExtract.jar"
-  out_file="$1/REMcRdy_lm_only.csv-finalTable.csv"
-
+  
   # backup REMcRdy_lm_only.csv-finalTable.csv
   if ! backup "$out_file"; then
     ask "Backup of $out_file failed, continue?" || return 1
@@ -1337,7 +1366,7 @@ java_extract() {
 
   debug "pushd && ${java_cmd[*]} && popd"
   pushd "$1" && "${java_cmd[@]}" && popd || return 1
-
+  out_file="$1/REMcRdy_lm_only.csv-finalTable.csv"
   [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
@@ -1345,17 +1374,22 @@ java_extract() {
 submodule r_add_shift_values
 # @description Add shift values back to REMcRdy_lm_only.csv-finalTable.csv
 # and output "REMcWithShift.csv" for use with the REMc heat maps
-# @arg $1 string The output csv file REMcRdy_lm_only.csv-finalTable.csv
+# @arg $1 string REMcRdy_lm_only.csv-finalTable.csv
 # @arg $2 string Shift_only.csv
-# @arg $3 string REMcWithShift.csv
+# @arg $3 string StudyInfo.csv file
 # @arg $4 string The sd value
 r_add_shift_values() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   script="$APPS_DIR/r/addShiftVals.R"
-  out_file="$QHTCP_PROJECT_DIR/REMcWithShift.csv"
   debug "$RSCRIPT $script $*"
-  "$RSCRIPT" "$script" "$@"
-  rm -f "REMcHeatmaps/"*.pdf
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "$2" \
+    "$3" \
+    "$4" \
+    "${@:5}" # optional arguments
+  rm -f "$QHTCP_PROJECT_DIR/REMcHeatmaps/"*.pdf
+  out_file="$QHTCP_PROJECT_DIR/REMcWithShift.csv"
   [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
@@ -1365,92 +1399,87 @@ submodule r_create_heat_maps
 # @arg $1 string The final shift table (REMcWithShift.csv)
 # @arg $2 string The output directory
 r_create_heat_maps() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   script="$APPS_DIR/r/createHeatMaps.R"
-  out_file="$QHTCP_PROJECT_DIR/compiledREMcHeatmaps.pdf"
   debug "$RSCRIPT $script $*"
-  "$RSCRIPT" "$script" "$@"
+  "$RSCRIPT" "$script" \
+    "$1" \
+    "$2" \
+    "${@:3}" # optional arguments
   pdfs=(REMcHeatmaps/*.pdf)
   debug "pdftk ${pdfs[*]} output $out_file"
   pdftk "${pdfs[@]}" output "$out_file"
+  out_file="$2/compiledREMcHeatmaps.pdf"
   [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
 
 submodule r_heat_maps_homology
 # @description Execute createHeatMapsAll.R
-# @arg $1 string The final shift table (REMcRdy_lm_only.csv-finalTable.csv)
-# @arg $2 string The (Shift_only.csv)
+# @arg $1 string REMcRdy_lm_only.csv-finalTable.csv
+# @arg $2 string Shift_only.csv
 # @arg $3 string The (Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv)
 # @arg $4 string The output directory
 r_heat_maps_homology() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   script="$APPS_DIR/r/createHeatMapsHomology.R"
-  out_file="$4/compiledREMcHomologyHeatmaps.pdf"
   
-  # Clean old output
+  # Remove old output
+  debug "Removing old pdfs and csvs from $4"
   rm "$4/"*.{pdf,csv}
 
   "$RSCRIPT" "$script" \
-    REMcWithShift.csv \
-    Homology \
-    "$APPS_DIR/r/170503_DAmPs_Only.txt" \
-    Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
+    "$1" \
+    "$2" \
+    "$3" \
+    "$4" \
+    "${@:5}" # optional arguments
 
   pdfs=("$work_dir"/homology/*.pdf)
   pdftk "${pdfs[@]}" output "$out_file"
-
+  out_file="$4/compiledREMcHomologyHeatmaps.pdf"
   [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
 
 submodule py_gtf_dcon
 # @description Perform python dcon portion of GTF
+# Output file:
+#   * 1-0-0-finaltable.csv
 # @arg $1 string Directory to process
 # @arg $2 string Output directory name
 py_gtf_dcon() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
+  debug "Running: ${FUNCNAME[0]} $*"
   script="$APPS_DIR/python/DconJG2.py"
-  debug "$PYTHON $SCRIPT $1 $2/"
-  "$PYTHON" "$SCRIPT" "$1" "$2/"
+  debug "$PYTHON $script $1 $2/"
+  "$PYTHON" "$script" \
+    "$1" \
+    "$2/" \
+    "${@:3}" # optional arguments
   out_file="$2/1-0-0-finaltable.csv"
   [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
 
-submodule pl_gtf
-# @description Perl modules for GTF
-# @arg $1 string Working directory
-# @arg $2 string Output directory name to look for txt files
-pl_gtf() {
-  debug "Running: ${FUNCNAME[0]}" "$@"
-  set1="$APPS_DIR/perl/ORF_List_Without_DAmPs.txt"
-  shopt -s nullglob
-  set2=("$2"/*.txt) # glob them all
-  shopt -u nullglob
-  for s2 in "${set2[@]}"; do
-    debug "pl_gtf_analyze $set1 $s2"
-    pl_gtf_analyze "$set1" "$s2"
-    debug "pl_terms2tsv $s2"
-    pl_gtf_terms2tsv "$s2"
-  done
-}
-
-
 submodule pl_gtf_analyze
 # @description Perl analyze submodule
 # This seems weird to me because we're just overwriting the same data for all set2 members
 # 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"