--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/averageFragSpectra.R	Wed Nov 27 12:41:53 2019 -0500
@@ -0,0 +1,165 @@
+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$method <- 'all'
+  }
+
+  combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
+
+  return(combined)
+}
+
+
+option_list <- list(
+  make_option("--out_rdata", type="character"),
+  make_option("--out_peaklist", type="character"),
+  make_option("--pa", type="character"),
+
+  make_option("--av_level", type="character"),
+
+  make_option("--minfrac", default=0.5),
+  make_option("--minnum", default=1),
+  make_option("--ppm", default=5.0),
+
+  make_option("--snr", default=0),
+
+  make_option("--ra", default=0),
+
+  make_option("--av", default="median", type="character"),
+  make_option("--sumi", action="store_true"),
+
+  make_option("--rmp", action="store_true"),
+  make_option("--cores", default=1)
+)
+
+opt <- parse_args(OptionParser(option_list=option_list))
+print(opt)
+
+
+loadRData <- function(rdata_path, name){
+#loads an RData file, and returns the named xset object if it is there
+    load(rdata_path)
+    return(get(ls()[ls() %in% name]))
+}
+
+# Requires
+pa <- loadRData(opt$pa, 'pa')
+
+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$avid <- 1:nrow(av_spectra)
+        
+        filenames <- sapply(av_spectra$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')
+
+  }
+}
+