Rollup for calculation_interaction_zscores refactor

workflow/qhtcp-workflow

@@ -1464,7 +1464,8 @@ wrapper calculate_interaction_zscores
 #
 # TODO
 #
-# * Needs simplification w/ StudyInfo, should we just use a studies dir and name the dir with study name?
+# * More variables can be read in from the config file to allow more configuration
+# * Add gene names, other threshold values, etc.
 #
 # INPUT
 #
@@ -1480,11 +1481,9 @@ wrapper calculate_interaction_zscores
 # *
 #
 # @arg $1 integer output directory
-# @arg $2 integer delta SD background value (default: 3) 
-# @arg $3 string study info file
-# @arg $4 string SGD_features.tab
-# @arg $5 string easy/results_std.txt
-# @arg $6 array pairs of experiment paths and names
+# @arg $2 string SGD_features.tab
+# @arg $3 string easy/results_std.txt
+# @arg $6 array triplets of experiment paths, names, sd threshold factor
 calculate_interaction_zscores() {
   debug "Running: ${FUNCNAME[0]} $*"
   cat <<-EOF
@@ -1499,7 +1498,7 @@ calculate_interaction_zscores() {
 		  * Background values are reported in the results sheet and so could also be analyzed there.
 	EOF
 
-  declare script="$APPS_DIR/r/calculate_interaction_zscores.R"
+  declare script="$APPS_DIR/r/calculate_interaction_zscores5.R"
   declare -a out_paths=("${1:-"$STUDY_RESULTS_DIR/zscores"}")
   for path in "${EXP_PATHS[@]}"; do
     out_paths+=("${path}/zscores")
@@ -1515,13 +1514,11 @@ calculate_interaction_zscores() {
     
   execute "$RSCRIPT" "$script" \
     "${1:-"$STUDY_RESULTS_DIR"}" \
-    "${2:-3}" \
-    "${3:-"$APPS_DIR/r/SGD_features.tab"}" \
-    "${4:-"$EASY_RESULTS_DIR/results_std.txt"}" \
-    "${@:5}" \
-    "${EXP_PATHS_AND_NAMES[@]}"
+    "${2:-"$APPS_DIR/r/SGD_features.tab"}" \
+    "${3:-"$EASY_RESULTS_DIR/results_std.txt"}" \
+    "${@:4}" \
+    "${EXP_PATHS_AND_NAMES_AND_SD_FACTORS[@]}"
 
-  [[ -f "$out_path/zscores_interaction.csv" ]] || (echo "$out_path/zscores_interaction.csv does not exist"; return 1)
 }
 
 
@@ -2136,6 +2133,21 @@ handle_config() {
     fi
   done
 
+  declare -ga EXP_PATHS_AND_NAMES_AND_SD_FACTORS
+  for key in "${!config_array_ref[@]}"; do
+    if [[ $key == *,path ]]; then
+      main_key="${key%,*}"
+      name_key="${main_key},name"
+      sd_key="${main_key},sd"
+      if [[ -n ${config_array_ref[$name_key]} ]]; then
+        EXP_PATHS_AND_NAMES_AND_SD_FACTORS+=(
+          "${config_array_ref[$key]}"
+          "${config_array_ref[$name_key]}"
+          "${config_array_ref[$sd_key]}")
+      fi
+    fi
+  done
+
   # declare -ga EXP_PATHS_AND_NAMES
   # for key in "${!config_array_ref[@]}"; do
   #   if [[ $key == *,path ]]; then