--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/averageFragSpectra.R	Thu Mar 04 12:12:45 2021 +0000
@@ -0,0 +1,155 @@
+library(optparse)
+library(msPurity)
+library(xcms)
+print(sessionInfo())
+
+
+get_av_spectra <- function(x) {
+
+  if (length(x$av_intra) > 0) {
+    av_intra_df <- plyr::ldply(x$av_intra)
+
+    if (nrow(av_intra_df) == 0) {
+      av_intra_df <- NULL
+    }else{
+      av_intra_df$method <- "intra"
+    }
+
+  }else{
+    av_intra_df <- NULL
+  }
+
+  if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
+    av_inter_df <- NULL
+  }else{
+    av_inter_df <- x$av_inter
+    av_inter_df$method <- "inter"
+  }
+
+  if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
+    av_all_df <- NULL
+  }else{
+    av_all_df <- x$av_all
+    av_all_df$method <- "all"
+  }
+
+  combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
+
+  return(combined)
+}
+
+
+option_list <- list(
+  make_option("--out_rdata", type = "character"),
+  make_option("--out_peaklist", type = "character"),
+  make_option("--pa", type = "character"),
+  make_option("--av_level", type = "character"),
+  make_option("--minfrac", default = 0.5),
+  make_option("--minnum", default = 1),
+  make_option("--ppm", default = 5.0),
+  make_option("--snr", default = 0),
+  make_option("--ra", default = 0),
+  make_option("--av", default = "median", type = "character"),
+  make_option("--sumi", action = "store_true"),
+  make_option("--rmp", action = "store_true"),
+  make_option("--cores", default = 1)
+)
+
+opt <- parse_args(OptionParser(option_list = option_list))
+print(opt)
+
+
+load_r_data <- function(rdata_path, name) {
+    #loads an RData file, and returns the named xset object if it is there
+    load(rdata_path)
+    return(get(ls()[ls() %in% name]))
+}
+
+# Requires
+pa <- load_r_data(opt$pa, "pa")
+
+pa@cores <- opt$cores
+
+if (is.null(opt$rmp)) {
+  rmp <- FALSE
+}else{
+  rmp <- TRUE
+}
+
+if (is.null(opt$sumi)) {
+  sumi <- FALSE
+}else{
+  sumi <- TRUE
+}
+
+if (opt$av_level == "intra") {
+  pa <- msPurity::averageIntraFragSpectra(pa,
+                                          minfrac = opt$minfrac,
+                                          minnum = opt$minnum,
+                                          ppm = opt$ppm,
+                                          snr = opt$snr,
+                                          ra = opt$ra,
+                                          av = opt$av,
+                                          sumi = sumi,
+                                          rmp = rmp,
+                                          cores = opt$cores)
+
+} else if (opt$av_level == "inter") {
+
+  pa <- msPurity::averageInterFragSpectra(pa,
+                                          minfrac = opt$minfrac,
+                                          minnum = opt$minnum,
+                                          ppm = opt$ppm,
+                                          snr = opt$snr,
+                                          ra = opt$ra,
+                                          av = opt$av,
+                                          sumi = sumi,
+                                          rmp = rmp,
+                                          cores = opt$cores)
+} else if (opt$av_level == "all") {
+
+  pa <- msPurity::averageAllFragSpectra(pa,
+                                        minfrac = opt$minfrac,
+                                        minnum = opt$minnum,
+                                        ppm = opt$ppm,
+                                        snr = opt$snr,
+                                        ra = opt$ra,
+                                        av = opt$av,
+                                        sumi = sumi,
+                                        rmp = rmp,
+                                        cores = opt$cores)
+}
+
+print(pa)
+save(pa, file = opt$out_rdata)
+
+if (length(pa) > 0) {
+
+  av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)
+
+  if (nrow(av_spectra) == 0) {
+    message("No average spectra available")
+  } else {
+    colnames(av_spectra)[1] <- "grpid"
+    av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]
+
+    if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
+      # Add some extra info (only required if av_intra or av_inter performed)
+      colnames(av_spectra)[2] <- "fileid"
+      av_spectra$avid <- seq_len(nrow(av_spectra))
+
+      filenames <- sapply(av_spectra$fileid,
+                          function(x) names(pa@fileList)[as.integer(x)])
+      # filenames_galaxy <- sapply(
+      #    av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
+
+        av_spectra <- as.data.frame(
+          append(av_spectra, list(filename = filenames), after = 2))
+    }
+
+
+    print(head(av_spectra))
+    write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
+
+  }
+}