annotate filterFragSpectra.R @ 1:0f646a3e0a3f draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"

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 <- 1: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')
  }
}