R/evidenceCheck.R

In mqqc: Quality control of LCMS derived proteomic data

evidenceCheck <- 
  function(hotFolder, matchType = "evimsms", sucFolder)
  {
    collectListPath <- paste(hotFolder,sucFolder,"list_collect.sqlite",sep = "/")
    if( file.exists(collectListPath)){
      collectList	<- 	dbreadfile(collectListPath)
      imported 		<- collectList[,dim(collectList)[2]]
      processed  <- unlist(lapply(strsplit(as.character(imported),"/combined"),function(x){return(x[1])}))
    }
    folders <- listFolders(hotFolder)
    folders <- grep("_RmqqcFile_",listFolders(hotFolder),fixed = T,value = T,invert = T)
    if(exists("processed")){
      try(folders <- setdiff(folders,processed))
    }
    if(length(folders)> 0){
      
      tempI <- list.files(folders,pattern = "Finish_writing_tables 11.finished",full.name = T,recursive = T)
      
      if(length(tempI) == 0){
        tempI <- list.files(folders,pattern = "evidence.txt",full.name = T,recursive = T)
        tempInoproc <- file.exists(paste(dirname(dirname(tempI)),"proc",sep = "/"))
        tempI <- tempI[!tempInoproc]
      }
      tempI <- grep("_RmqqcFile_",tempI,invert = T,value = T,fixed = T)
      tempI <- list.files(dirname(dirname(tempI)),pattern = "evidence.txt",recursive = T,full.names = T)
      #tempI <- paste(folders, tempI,sep = "")
      #finishTables  <- list.files(paste(dirname(dirname(tempI)),"proc",sep = "/"),pattern = "Finish_writing_tables 11.finished",full.name = T)
      
      if(matchType == "evimsms"& length(tempI) > 1 ){
        tempiSel <-     sapply(tempI,function(x){
          fi <- paste(dirname(x),"#runningTimes.txt",sep = "/")
          if(file.exists(fi)){
            RunTi <- read.csv(fi,sep = "\t",stringsAsFactors = F)
            
            return(nchar(RunTi$End.time[RunTi$Job == "Finish writing tables  "]) >=7)
          }else{T}
        })
        tempI <- tempI[tempiSel]
        tempI <- paste(dirname(dirname(tempI)),"txt/evidence.txt",sep = "/")
        #       tempI <- gsub("//","/",tempI)
        #     
        #    		msms          <- list.files(dirname(tempI),pattern = "msms.txt",full.name = T,recursive = T)	
        #    		if(length(msms) != 0){
        #     		tempIt <- intersect(dirname(tempI),dirname(msms))  			
        #    			if(length(tempIt) > 0){
        #  	  		tempI <- paste(tempIt,"evidence.txt",sep = "/")
        #    			}   		
        #    		}
        
        
      }
      
      mqqcInfo <- NULL
      if(length(tempI)> 0){
        # Check if evidence was already processed if yes, no output of evidence path
        mqqcInfo <- c()
        for(i in 1:length(tempI)){
          tempI <<- tempI
          tempmqqcInfo  <- list.files(dirname(tempI[i]),pattern = "mqqc",full.name = T)
          if(length(tempmqqcInfo)==0){
            mqqcInfo    <- c(mqqcInfo,tempI[i])
          }else{
          }
        }
        # mqqcInfo 	<- mqqcInfo[file.info(mqqcInfo)$isdir]
        
      }
    }else{mqqcInfo <- NULL}
    return(mqqcInfo)
  }
# evidenceCheck(folder,sucFolder = "_RmqqcFile_Processed")