Modularize joinInteractExps.R
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@@ -380,7 +380,6 @@ init_project() {
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ask "Initialize a project at $SCANS_DIR?" || return 1
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# Write skeleton files in csv
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# If we have to convert to xlsx later, so be it
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cat <<-EOF > "$DRUG_MEDIA_FILE"
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@@ -398,9 +397,6 @@ init_project() {
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# TODO here we'll copy scan from robot but for now let's pause and wait for transfer
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read -r -p "Hit <Enter> to continue: "
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}
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@@ -673,11 +669,12 @@ module qhtcp
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qhtcp() {
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debug "Running: ${FUNCNAME[0]}"
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QHTCP_BASE_DIR="/mnt/data/StudiesQHTCP"
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QHTCP_PROJECT_DIR="$QHTCP_BASE_DIR/$PROJECT"
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CODE_DIR="$QHTCP_PROJECT_DIR/Code"
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STUDIES_ARCHIVE_FILE="$QHTCP_BASE_DIR/StudiesDataArchive.txt"
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STUDY_INFO_FILE="$CODE_DIR/StudyInfo.csv"
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OUT_DIR="/mnt/data/out/qhtcp"
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STUDIES_ARCHIVE_FILE="$OUT_DIR/StudiesDataArchive.txt"
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QHTCP_PROJECT_DIR="$OUT_DIR/$PROJECT"
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APPS_DIR="$QHTCP_PROJECT_DIR/apps"
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CODE_DIR="$QHTCP_PROJECT_DIR/Code" # legacy location, keeping until can port each script to APPS
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STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
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if [[ -d $QHTCP_PROJECT_DIR ]]; then
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echo "A project already exists at $QHTCP_PROJECT_DIR"
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@@ -735,8 +732,10 @@ qhtcp() {
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fi
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# Initialize missing dirs
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STUDIES_DIRS=()
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for s in "${STUDIES_NUMS[@]}"; do
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STUDY_DIR="$QHTCP_PROJECT_DIR/Exp$s"
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STUDIES_DIRS+=("$STUDY_DIR")
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if ! [[ -d $STUDY_DIR ]]; then
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if ! rsync --archive "$STUDY_TEMPLATE_DIR" "$STUDY_DIR"; then
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err "Could not copy $STUDY_TEMPLATE_DIR template to $STUDY_DIR"
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@@ -788,18 +787,17 @@ qhtcp() {
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# Run R interactions script on all studies
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for s in "${STUDIES_NUMS[@]}"; do
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STUDY_DIR="$QHTCP_PROJECT_DIR/Exp$s"
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pushd "$STUDY_DIR" || return 1
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r_interactions \
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"$STUDY_DIR"\
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"$STUDY_INFO_FILE"\
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"/ZScores/" \
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"$STUDY_DIR" \
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"$STUDY_INFO_FILE" \
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"$STUDY_DIR/ZScores/" \
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"$CODE_DIR/SGD_features.tab" \
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5
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popd || return 1
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done
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# Run remc as part of the QHTCP process
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remc
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# pass all the study directories to it so the scripts have all the paths
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remc "$STUDY_INFO_FILE" "${STUDIES_DIRS[@]}"
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}
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@@ -814,7 +812,7 @@ module remc
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# * Use arguments to pass configuration variables
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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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remc() {
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debug "Running: ${FUNCNAME[0]}"
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debug "Running: ${FUNCNAME[0]}" "$@"
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# Enter REMc directory to run the scripts there
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pushd "$QHTCP_PROJECT_DIR/REMc" || return 1
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@@ -823,7 +821,7 @@ remc() {
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# If any modules fail the rest will not run, this is fundamental to module design
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# Remove trailing && to run regardless
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# TODO can this be
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r_join_interact &&
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r_join_interactions "$QHTCP_PROJECT_DIR/1-join_interactions" 2 "$1" "${@:2}" &&
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java_extract &&
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r_add_shift_values &&
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r_heat_maps_zscores &&
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@@ -1131,22 +1129,25 @@ r_interactions() {
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This is most often "trial and error", meaning there is a 'Frequency_Delta_Background.pdf' report in the /Exp_/ZScores/QC/ folder to evaluate whether the chosen value was suitable (and if not the analysis can simply be rerun with a more optimal choice). In general, err on the high side, with BSD of 10 or 12…. One can also use EZview to examine the raw images and individual cultures potentially included/excluded as a consequence of the selected value. Background values are reported in the results sheet and so could also be analyzed there..
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EOF
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script="Z_InteractionTemplate.R"
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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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}
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submodule r_join_interact
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submodule r_join_interactions
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# @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
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r_join_interact() {
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debug "Running: ${FUNCNAME[0]}"
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debug "$RSCRIPT JoinInteractExps3dev.R"
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"$RSCRIPT" JoinInteractExps3dev.R
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out_file="REMcRdy_lm_only.csv"
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out_file2="Shift_only.csv"
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for f in "$out_file" "$out_file2"; do
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# @arg $1 string The output directory
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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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script="$APPS_DIR/r/joinInteractExps.R"
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debug "$RSCRIPT $script"
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"$RSCRIPT" "$script" "$@"
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local out_files=("REMcRdy_lm_only.csv" "Shift_only.csv" "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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done
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}
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@@ -1427,7 +1428,7 @@ main() {
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# Global directory variables
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TEMPLATES_DIR="$SCRIPT_DIR/templates"
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QHTCP_TEMPLATE_DIR="$TEMPLATES_DIR/qhtcp"
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STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/demo"
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STUDY_TEMPLATE_DIR="$QHTCP_TEMPLATE_DIR/ExpTemplate"
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EASY_DIR="$SCRIPT_DIR/apps/matlab/easy"
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DATE="$(date +%Y%m%d)" # change in EASYConsole.m to match
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SCANS="${SCANS:-"./scans":-"/mnt/data/ExpJobs"}"
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@@ -1501,7 +1502,6 @@ main() {
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PROJECT_DATE="${PROJECT%"${PROJECT#????????}"}" # e.g. 20240723
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PROJECT_SUFFIX="${PROJECT#????????_*_}"
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PROJECT_USER="${PROJECT#????????_}"; PROJECT_USER="${PROJECT_USER%%_*}"
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PROJECT_NAME="${PROJECT_DATE}_${PROJECT_USER}_${PROJECT_SUFFIX}"
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# Run selected modules
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for m in "${MODULES[@]}"; do
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ask "Run $m" && "$m"
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