--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filterFragSpectra.R	Thu Mar 04 12:17:52 2021 +0000
@@ -0,0 +1,99 @@
+library(optparse)
+library(msPurity)
+library(xcms)
+print(sessionInfo())
+
+
+option_list <- list(
+  make_option("--out_rdata", type = "character"),
+  make_option("--out_peaklist_prec", type = "character"),
+  make_option("--out_peaklist_frag", type = "character"),
+  make_option("--pa", type = "character"),
+
+  make_option("--ilim", default = 0.0),
+  make_option("--plim", default = 0.0),
+
+  make_option("--ra", default = 0.0),
+  make_option("--snr", default = 0.0),
+
+  make_option("--rmp", action = "store_true"),
+  make_option("--snmeth", default = "median", type = "character")
+)
+
+opt <- parse_args(OptionParser(option_list = option_list))
+print(opt)
+
+
+loadRData <- 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 <- loadRData(opt$pa, "pa")
+
+if (is.null(opt$rmp)) {
+  opt$rmp <- FALSE
+}else{
+  opt$rmp <- TRUE
+}
+
+pa <- filterFragSpectra(pa,
+                        ilim = opt$ilim,
+                        plim = opt$plim,
+                        ra = opt$ra,
+                        snr = opt$snr,
+                        rmp = opt$rmp,
+                        snmeth = opt$snmeth)
+
+print(pa)
+save(pa, file = opt$out_rdata)
+
+# get the msms data for grpid from the purityA object
+msmsgrp <- function(grpid, pa) {
+  msms <- pa@grped_ms2[grpid]
+
+  grpinfo <- pa@grped_df[pa@grped_df$grpid == grpid, ]
+
+  grpinfo$subsetid <- seq_len(nrow(grpinfo))
+  result <- plyr::ddply(grpinfo, ~subsetid, setid, msms = msms)
+  return(result)
+}
+
+# Set the relevant details
+setid <- function(grpinfo_i, msms) {
+  msms_i <- msms[[1]][[grpinfo_i$subsetid]]
+  n <- nrow(msms_i)
+  msms_i <- data.frame(msms_i)
+  colnames(msms_i)[1:2] <- c("mz", "i")
+  m <- cbind("grpid" = rep(grpinfo_i$grpid, n), "pid" = rep(grpinfo_i$pid, n), "fileid" = rep(grpinfo_i$fileid, n), msms_i)
+  return(m)
+}
+
+
+
+if (length(pa) > 0) {
+
+  if (length(pa@grped_ms2) == 0) {
+    message("No spectra available")
+  } else {
+
+    # get group ids
+    grpids <- unique(as.character(pa@grped_df$grpid))
+
+    # loop through all the group ids
+    df_fragments <- plyr::adply(grpids, 1, msmsgrp, pa = pa)
+    df_fragments <- merge(df_fragments, pa@puritydf[, c("pid", "acquisitionNum", "precursorScanNum")], by = "pid")
+    df_fragments <- df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz), ]
+    #select and reorder columns
+    df_fragments <- df_fragments[, c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")]
+
+    pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)])
+
+    print(head(pa@grped_df))
+    write.table(pa@grped_df, opt$out_peaklist_prec, row.names = FALSE, sep = "\t")
+    print(head(df_fragments))
+    write.table(df_fragments, opt$out_peaklist_frag, row.names = FALSE, sep = "\t")
+  }
+}