Rollup before java debug
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@@ -26,8 +26,8 @@ args <- parse_arguments()
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# Create an array for the zscores files
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get_zscores_files <- function(dirs) {
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files <- sapply(dirs, function(study) {
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file_path <- file.path(study, "zscores", "zscores_interaction.csv")
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files <- sapply(dirs, function(exp) {
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file_path <- file.path(exp, "zscores", "zscores_interaction.csv")
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if (file.exists(file_path)) file_path else NULL
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}, simplify = TRUE, USE.NAMES = FALSE)
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113
workflow/apps/r/join_interaction_zscores.R
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113
workflow/apps/r/join_interaction_zscores.R
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@@ -0,0 +1,113 @@
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suppressMessages({
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library("dplyr")
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library("data.table")
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library("readr")
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library("stringr")
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})
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# Function to parse arguments
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parse_arguments <- function() {
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if (interactive()) {
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args <- c(
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"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD",
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3, # sd value
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"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp1",
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"Experiment 1: Doxo versus HLD",
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"/home/bryan/documents/develop/scripts/hartmanlab/workflow/out/20240116_jhartman2_DoxoHLD/20240822_jhartman2_DoxoHLD/exp2",
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"Experiment 2: HLD versus Doxo"
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)
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} else {
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args <- commandArgs(trailingOnly = TRUE)
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}
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out_dir <- normalizePath(args[1], mustWork = FALSE)
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sd <- as.numeric(args[2])
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paths <- normalizePath(args[seq(3, length(args), by = 2)], mustWork = FALSE)
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names <- args[seq(4, length(args), by = 2)]
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experiments <- setNames(paths, names)
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list(
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out_dir = out_dir,
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sd = sd,
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experiments = experiments
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)
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}
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args <- parse_arguments()
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# Ensure main output directory exists
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dir.create(args$out_dir, showWarnings = FALSE, recursive = TRUE)
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# Function to read and combine z-score interaction files
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combine_zscores <- function(experiments, out_dir) {
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combined_data <- lapply(names(experiments), function(exp_name) {
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exp_dir <- experiments[[exp_name]]
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zscore_file <- file.path(exp_dir, "zscores", "zscores_interaction.csv")
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if (!file.exists(zscore_file)) {
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stop("Z-score file does not exist for ", exp_name, " at ", zscore_file)
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}
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message("Reading z-score file for ", exp_name, " from ", zscore_file)
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data <- fread(zscore_file)
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data$Experiment <- exp_name
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return(data)
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}) %>%
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bind_rows()
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combined_output_file <- file.path(out_dir, "combined_zscores.csv")
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fwrite(combined_data, combined_output_file, row.names = FALSE)
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message("Combined z-score file saved to: ", combined_output_file)
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}
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# Function to read and combine summary statistics files
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combine_summary_stats <- function(experiments, out_dir) {
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combined_stats <- lapply(names(experiments), function(exp_name) {
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exp_dir <- experiments[[exp_name]]
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summary_file <- file.path(exp_dir, "zscores", "summary_stats_all_strains.csv")
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if (!file.exists(summary_file)) {
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stop("Summary stats file does not exist for ", exp_name, " at ", summary_file)
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}
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message("Reading summary stats file for ", exp_name, " from ", summary_file)
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data <- fread(summary_file)
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data$Experiment <- exp_name
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return(data)
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}) %>%
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bind_rows()
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combined_output_file <- file.path(out_dir, "combined_summary_stats.csv")
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fwrite(combined_stats, combined_output_file, row.names = FALSE)
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message("Combined summary stats file saved to: ", combined_output_file)
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}
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# Function to generate final summary report
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generate_final_report <- function(out_dir) {
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combined_zscores <- file.path(out_dir, "combined_zscores.csv")
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combined_stats <- file.path(out_dir, "combined_summary_stats.csv")
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if (!file.exists(combined_zscores) || !file.exists(combined_stats)) {
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stop("Combined z-scores or summary stats files do not exist.")
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}
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zscores_data <- fread(combined_zscores)
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stats_data <- fread(combined_stats)
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message("Merging z-score and summary stats data...")
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final_report <- merge(zscores_data, stats_data, by = c("OrfRep", "Experiment"), all = TRUE, allow.cartesian = TRUE)
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final_report_file <- file.path(out_dir, "final_combined_report.csv")
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fwrite(final_report, final_report_file, row.names = FALSE)
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message("Final combined report saved to: ", final_report_file)
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}
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# Process all experiments and generate outputs
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combine_zscores(args$experiments, args$out_dir)
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combine_summary_stats(args$experiments, args$out_dir)
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generate_final_report(args$out_dir)
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@@ -1296,6 +1296,7 @@ qhtcp() {
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# Run R interactions script on all studies
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calculate_interaction_zscores \
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&& join_interaction_zscores \
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&& remc \
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&& gtf \
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&& gta
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@@ -1316,7 +1317,6 @@ remc() {
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# If any wrappers 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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#r_join_interactions \
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java_extract \
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&& r_add_shift_values \
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&& r_create_heat_maps \
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@@ -1522,7 +1522,50 @@ calculate_interaction_zscores() {
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"${EXP_PATHS_AND_NAMES[@]}"
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[[ -f "$out_path/zscores_interaction.csv" ]] || (echo "$out_path/zscores_interaction.csv does not exist"; return 1)
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((DEBUG)) && declare -p && exit # when the going gets rough
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}
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wrapper join_interaction_zscores
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# shellcheck disable=SC2120
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# @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
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#
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# TODO
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#
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# * Needs more loops to reduce verbosity
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#
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# INPUT
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#
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# * /out/PROJECT/STUDY/exp#/zscores/zscores_interaction.csv
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#
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# OUTPUT
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#
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# * combined_zscores.csv (REMcRdy_lm_only.csv)
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# * combined_summary_stats (Shift_only.csv)
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# * final_combined_report (parameters.csv)
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#
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# @arg $1 string output directory
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# @arg $2 string sd value (default: 2)
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# @arg $3 array pairs of experiment paths and names
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join_interaction_zscores() {
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debug "Running: ${FUNCNAME[0]} $*"
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declare script="$APPS_DIR/r/join_interaction_zscores.R"
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declare -a out_files=(
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"${1:-$STUDY_RESULTS_DIR}/combined_zscores.csv"
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"${1:-$STUDY_RESULTS_DIR}/combined_summary_stats.csv"
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"${1:-$STUDY_RESULTS_DIR}/final_combined_report.csv"
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)
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# ((DEBUG)) && declare -p # when the going gets tough
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execute "$RSCRIPT" "$script" \
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"${1:-$STUDY_RESULTS_DIR}" \
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"${2:-2}" \
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"${@:3:}" \
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"${EXP_PATHS_AND_NAMES[@]}"
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for f in "${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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@@ -1671,52 +1714,6 @@ r_gta_heatmaps() {
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}
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# wrapper r_join_interactions
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# # shellcheck disable=SC2120
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# # @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
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# #
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# # TODO
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# #
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# # * Needs more loops to reduce verbosity
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# #
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# # INPUT
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# #
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# # * study info file
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# # * /out/PROJECT/STUDY/exp#/zscores/zscores_interaction.csv
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# #
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# # OUTPUT
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# #
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# # * REMcRdy_lm_only.csv
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# # * Shift_only.csv
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# # * parameters.csv
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# #
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# # @arg $1 string output directory (required)
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# # @arg $2 string sd value (default: 2) (required)
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# # @arg $3 string study info file (required)
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# # @arg $4 array studies (required)
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# r_join_interactions() {
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# debug "Running: ${FUNCNAME[0]} $*"
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# declare script="$APPS_DIR/r/joinInteractExps.R"
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# declare -a out_files=(
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# "${1:-$STUDY_RESULTS_DIR}/REMcRdy_lm_only.csv"
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# "${1:-$STUDY_RESULTS_DIR}/Shift_only.csv"
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# "${1:-$STUDY_RESULTS_DIR}/parameters.csv"
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# )
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# # ((DEBUG)) && declare -p # when the going gets tough
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# execute "$RSCRIPT" "$script" \
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# "${1:-$STUDY_RESULTS_DIR}" \
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# "${2:-2}" \
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# "${3:-$STUDY_INFO_FILE}" \
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# "${@:4:-${EXP_PATHS[@]}}"
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# for f in "${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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wrapper java_extract
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# shellcheck disable=SC2120
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# @description Jingyu's REMc java utility
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@@ -1727,14 +1724,14 @@ wrapper java_extract
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#
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# INPUT
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#
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# * REMcRdy_lm_only.csv
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# * study_dir/combined_zscores.csv (REMcRdy_lm_only.csv)
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#
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# OUTPUT
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#
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# * REMcRdy_lm_only.csv-finalTable.csv
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# * study_dir/combined_zscores_final.csv (REMcRdy_lm_only.csv-finalTable.csv)
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#
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# @arg $1 string output directory
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# @arg $2 string REMcRdy_lm_only.csv
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# @arg $2 string combined_zscores.csv
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# @arg $3 string GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab
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# @arg $4 string ORF_List_Without_DAmPs.txt
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# @exitcode 0 if expected output file exists
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@@ -1743,14 +1740,14 @@ java_extract() {
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debug "Running: ${FUNCNAME[0]}"
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classpath="$APPS_DIR/java/weka-clustering/weka-clustering.jar"
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output_file="${1:-$STUDY_RESULTS_DIR}/REMcRdy_lm_only.csv-finalTable.csv"
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output_file="${1:-$STUDY_RESULTS_DIR}/combined_zscores_final.csv"
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[[ -f $output_file ]] && backup "$output_file"
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java_cmd=(
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"$JAVA" -Xms512m -Xmx2048m -Dfile.encoding=UTF-8
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-classpath "$classpath" ExecMain
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"${2:-"$STUDY_RESULTS_DIR/REMcRdy_lm_only.csv"}"
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"${2:-"$STUDY_RESULTS_DIR/combined_zscores.csv"}"
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"${3:-"$APPS_DIR/java/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab"}"
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"${4:-"$APPS_DIR/java/ORF_List_Without_DAmPs.txt"}"
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1
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@@ -2297,9 +2294,9 @@ main() {
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# Sanitize wrappers
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for i in "${!WRAPPERS[@]}"; do
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IFS=',' read -ra args <<< "$wrapper" # load the wrapper and args
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IFS=',' read -ra args <<< "${WRAPPERS[$i]}" # load the wrapper and args
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if ! [[ " ${ALL_WRAPPERS[*]} " =~ [[:space:]]${args[0]}[[:space:]] ]]; then
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echo "Wrapper ${WRAPPERS[$i]} is not available, removing"
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echo "Wrapper ${args[0]} is not available, removing"
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unset "WRAPPERS[$i]"
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fi
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done
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