Improve get_studies

workflow/qhtcp-workflow

@@ -1280,60 +1280,9 @@ qhtcp() {
     done
   fi
 
-  # Sets STUDIES_NUMS and NUM_STUDIES (yes this makes sense)
+  # Sets STUDIES_NUMS
   get_studies "$STUDY_INFO_FILE"
 
-  # Construct the next auto-entry
-  # 1,ExpName1,NA,NA,UserInitials
-  next_study_num=$(( NUM_STUDIES + 1 ))
-
-  # If the next Exp dir already exists don't use it
-  while [[ -d $QHTCP_PROJECT_DIR/Exp$next_study_num ]]; do
-    (( next_study_num++ ))
-  done
-
-  # Use initials from project or whoami?
-  # Best I can do is first two letters of username
-  # See TODO in markdown
-  initials="${USER:0:2}"
-  INITIALS=${initials^^}
-  next_study_entry="$next_study_num,$PROJECT_SUFFIX,NA,NA,$INITIALS"
-  debug "$next_study_entry"
-
-  # Print current studies
-  [[ -f $STUDY_INFO_FILE ]] && 
-  echo "Current studies from $STUDY_INFO_FILE: " &&
-  cat "$STUDY_INFO_FILE"
-  
-  # Ask user to edit STUDY_INFO_FILE
-  if ! ((YES)) && ask "Would you like to edit $STUDY_INFO_FILE to add or modify studies?"; then
-    cat <<-EOF 
-			Give each experiment labels to be used for the plots and specific files. 
-			Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
-
-			Auto-entry suggestion: $next_study_entry
-		EOF
-    if ask "Would you like to add (y) the auto-entry suggestion to $STUDY_INFO_FILE or edit STUDY_INFO_FILE in nano (n)?"; then
-      echo "$next_study_entry" >> "$STUDY_INFO_FILE"
-    else
-      debug "nano $STUDY_INFO_FILE"
-      nano "$STUDY_INFO_FILE"
-    fi
-  fi
-
-  # Initialize missing dirs
-  STUDIES_DIRS=()
-  for s in "${STUDIES_NUMS[@]}"; do
-    STUDY_DIR="$QHTCP_PROJECT_DIR/Exp$s"
-    STUDIES_DIRS+=("$STUDY_DIR")
-    if ! [[ -d $STUDY_DIR ]]; then
-      if ! rsync --archive "$STUDY_TEMPLATE_DIR" "$STUDY_DIR"; then
-        err "Could not copy $STUDY_TEMPLATE_DIR template to $STUDY_DIR"
-        continue
-      fi
-    fi
-  done
-  unset STUDY_DIR
 
   # Replacing ExpFrontend.m
   choose_easy_results_dir
@@ -1391,7 +1340,11 @@ remc() {
     "$1" # studyInfo file
     "${@:2}" \
   && java_extract \
-    "$QHTCP_PROJECT_DIR/out/" \
+    "$APPS_DIR/java/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab" \
+    "$APPS_DIR/java/ORF_List_Without_DAmPs.txt" \
+    "$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv" \
+    "$QHTCP_PROJECT_DIR" \
+    "$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv" \
   && r_add_shift_values \
     "$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv" \
     "$QHTCP_PROJECT_DIR/Shift_only.csv" \
@@ -1399,7 +1352,7 @@ remc() {
     "$QHTCP_PROJECT_DIR/REMcWithShift.csv" \
   && r_create_heat_maps \
     "$QHTCP_PROJECT_DIR/REMcWithShift.csv" \
-    "$QHTCP_PROJECT_DIR/out" \
+    "$QHTCP_PROJECT_DIR" \
   && r_heat_maps_homology \
     "$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv" \
     "$APPS_DIR/r/170503_DAmPs_Only.txt" \
@@ -1483,7 +1436,7 @@ gta() {
   all_sgd_terms_csv="${5:-"$APPS_DIR/r/All_SGD_GOTerms_for_QHTCPtk.csv"}" 
   zscores_file="${6:-"$gta_out_dir/zscores/zscores_interaction.csv"}" # TODO This could be wrong, it could be in main results
     
-  # Sets STUDIES_NUM and NUM_STUDIES
+  # Sets STUDIES_NUMS
   get_studies "$STUDY_INFO_FILE"
 
   [[ -d $gta_out_dir ]] || mkdir "$gta_out_dir"
@@ -1631,7 +1584,7 @@ submodule r_gta_pairwiselk
 #
 # @arg $1 string First Exp# name
 # @arg $2 string Second Exp# name
-# @arg $3 string StudyInfo.txt file
+# @arg $3 string StudyInfo.csv file
 # @arg $4 string output directory
 #
 r_gta_pairwiselk() {
@@ -1772,27 +1725,33 @@ submodule java_extract
 #
 # * Closed-source w/ hardcoded output directory, so have to pushd/popd to run (not ideal)
 #
-# @arg $1 string The output directory
+# @arg $1 string GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab
+# @arg $2 string ORF_List_Without_DAmPs.txt
+# @arg $3 string REMcRdy_lm_only.csv
+# @arg $4 string The output directory
+# @arg $5 string The output file
+# @exitcode 0 if expected output file exists
+# @exitcode 1 if expected output file does not exist
+
 java_extract() {
   debug "Running: ${FUNCNAME[0]}"
   classpath="$APPS_DIR/java/javaExtract.jar"
   
-  # backup REMcRdy_lm_only.csv-finalTable.csv
+  # backup previous output
-  if ! backup "$out_file"; then
+  if ! backup "${5:-"$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv"}"; then
-    ask "Backup of $out_file failed, continue?" || return 1
+    ask "Backup of ${5:-"$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv"} failed, continue?" || return 1
   fi
 
   java_cmd=(
     "$JAVA" -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath "$classpath" ExecMain
-    "$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv"
+    "${3:-"$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv"}"
-    "$APPS_DIR/java/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab"
+    "${1:-"$APPS_DIR/java/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab"}"
-    "$APPS_DIR/java/ORF_List_Without_DAmPs.txt" 1 true true
+    "${2:-"$APPS_DIR/java/ORF_List_Without_DAmPs.txt"}"
   )
 
   debug "pushd && ${java_cmd[*]} && popd"
-  pushd "$1" && "${java_cmd[@]}" && popd || return 1
+  pushd "${4:-"$QHTCP_PROJECT_DIR"}" && "${java_cmd[@]}" && popd || return 1
-  out_file="$1/REMcRdy_lm_only.csv-finalTable.csv"
+  [[ -f ${5:-$QHTCP_PROJECT_DIR/REMcRdy_lm_only.csv-finalTable.csv} ]]
-  [[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
 }
 
 
@@ -1964,18 +1923,94 @@ submodule get_studies
 # @exitcode 0 If one or more studies found
 # @exitcode 1 If no studies found
 # @set STUDIES_NUMS array Contains Exp numbers
-# @set NUM_STUDIES int Number of existing studies
 # @arg $1 string File to read
 #
 get_studies() {
   debug "Running: ${FUNCNAME[0]}"
   declare -ga STUDIES_NUMS=()
+  # Use initials from project or whoami?
+  # Best I can do is first two letters of username
+  # See TODO in markdown
+  initials="${USER:0:2}"
+  INITIALS=${initials^^}
+  empty_study=0
+
+  # Find an Exp directory that does not exist
+  while [[ -d $QHTCP_PROJECT_DIR/Exp$empty_study ]]; do
+    (( empty_study++ ))
+  done
+
+  next_study_entry="$empty_study,$PROJECT_SUFFIX,NA,NA,$INITIALS"
+
+  if [[ ! -f $1 ]]; then
+    echo "Creating default $1"
+    echo "ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy" > "$1"
+    echo "$next_study_entry" >> "$1"
+    next_study_entry="$((empty_study+1)),$PROJECT_SUFFIX,NA,NA,$INITIALS"
+  fi
+
+  # Print current studies
+  cat <<-EOF 
+		Give each experiment labels to be used for the plots and specific files. 
+		Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
+
+		Current StudyInfo file ($1) contents:
+
+		$(cat "$S1")
+	EOF
+
+  # Allow user to add/edit the study info file
+  if ! ((YES)); then
+    for ((i=1; i<2; i++)); do
+      echo "Auto-entry suggestion: $next_study_entry"
+      echo "Would you like to (a)dd the auto-entry, (e)dit the StudyInfo.csv file in nano, or (c)ontinue?"
+      read -r -p "Hit [Enter] or c to continue: " response
+      [[ -z $response ]] && break
+      case $response in
+        a)
+          echo "Adding auto-entry suggestion to $1"
+          echo "$next_study_entry" >> "$1"
+          next_study_entry="$((empty_study+1)),$PROJECT_SUFFIX,NA,NA,$INITIALS"
+          i=0
+          ;;
+        e)
+          debug "nano $1"
+          nano "$1"
+          ;;
+        c)
+          break
+          ;;
+        *)
+          err "Invalid response, please try again"
+          i=0
+          ;;
+      esac
+      break
+    done
+  fi
+
+  # Read study info file
   while IFS=',' read -r col1 _; do # split on comma, get second col
     STUDIES_NUMS+=("$col1")
   done < <(tail -n +2 "$1") # skip header
 
-  [[ ${#STUDIES_NUMS[@]} -gt 0 ]] &&
+  [[ ${#STUDIES_NUMS[@]} -gt 0 ]]
-  NUM_STUDIES="${#STUDIES_NUMS{@}}"
+
+  # Initialize missing dirs
+  STUDIES_DIRS=()
+  for s in "${STUDIES_NUMS[@]}"; do
+    STUDY_DIR="$QHTCP_PROJECT_DIR/Exp$s"
+    STUDIES_DIRS+=("$STUDY_DIR")
+    [[ -d $STUDY_DIR ]] || mkdir "$STUDY_DIR"
+    # # We don't need a template anymore?
+    #   if ! rsync --archive "$STUDY_TEMPLATE_DIR" "$STUDY_DIR"; then
+    #     err "Could not copy $STUDY_TEMPLATE_DIR template to $STUDY_DIR"
+    #     continue
+    #   fi
+    # fi
+  done
+  unset STUDY_DIR
+
 }
 
 
@@ -2177,7 +2212,6 @@ main() {
     declare -gx STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
     declare -gx QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT_NAME"
     declare -gx QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
-    declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
     declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
     declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy"
     declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
@@ -2186,7 +2220,7 @@ main() {
       PROJECTS PROJECT_NAME \
       PROJECT_SCANS_DIR PROJECT_DATE PROJECT_SUFFIX PROJECT_USER \
       STUDIES_ARCHIVE_FILE QHTCP_PROJECT_DIR QHTCP_TEMPLATE_DIR \
-      STUDY_TEMPLATE_DIR STUDY_INFO_FILE
+      STUDY_INFO_FILE
     fi
 
     debug "Active modules: ${MODULES[*]}"