QFA_ANALYSIS_LIST.R

# To execute this script manually, in parallel on multiple CPUs:
# Rscript Scripts/QFA_ANALYSIS_INDIVIDUAL.R QFA0028 QFA0029 &
# Rscript Scripts/QFA_ANALYSIS_INDIVIDUAL.R QFA0030 QFA0031 &
library(parallel)
source("Scripts/QFA_ANALYSIS.R")
PLOSGenetics=sprintf("QFA%04d",c(28,29,30,31,35,36))

# NCPUs is the maximum number of CPUs the script can use on this node (should be less than 48 on cisban cluster)
NCPUs=47
cisbanNodes=TRUE

# Optionally spcify files for analysis here
#flist=c("QFA0135")
#flist=sprintf("QFA%04d",1:16)
#flist=sprintf("QFA%04d",c(28,29,30,31,35,36))
flist=sprintf("QFA%04d",c(6,10,11,12,18)) # Marion's expts
# Try lots of different AUClim
QFA_nAUCdef=function() {
        times=seq(0.2,5.0,0.2)
        return(function(cfolder,modelFit) QFA_analysis(cfolder=cfolder,modelFit=modelFit,AUClim=times))
}
QFA_nAUC=QFA_nAUCdef()

# If any experiments specified in command line, use those instead of flist specified above
args <- commandArgs(trailingOnly = TRUE)
if(length(args)>0){
        flist=args
}

# Discard experiments without the relevant directories
flist=flist[file.exists(file.path("QFA_EXPERIMENTS",flist))]
Nlist=length(flist)

if(length(args)>0){
  #for(f in flist) QFA_analysis(f)
  for(f in flist) QFA_nAUC(cfolder=f,modelFit=TRUE)
}else{
  # Read image logs and carry out model fitting
  if(cisbanNodes){
        actCPUs=min(Nlist,NCPUs) # detectCores() to find number of CPUs on local machine...
        nodes=c("cisban-node3","cisban-node2","cisban-node1")
        nodes=sort(rep(nodes,16),decreasing=TRUE)
  }else{
        actCPUs=min(detectCores()-1,Nlist,NCPUs)
        nodes=rep("localhost",actCPUs)
  }
  print(paste("Attempting to analyse files:",flist))
  cl <- makePSOCKcluster(nodes[1:actCPUs])
        clusterEvalQ(cl,library(qfa))
        if(cisbanNodes) clusterEvalQ(cl,setwd("/home/yeastimages/LOGS3"))
        clusterEvalQ(cl,source("Scripts/QFA_ANALYSIS.R"))
        #clusterApply(cl,flist,QFA_analysis,AUClim=AUCs,glog=TRUE,elab=elabs,modelFit=FALSE)
        clusterApply(cl,flist,QFA_nAUC,modelFit=TRUE)
  stopCluster(cl)

  makeImBrowser=function(barcode,imtime=2.0,skipDone=TRUE){
        string=paste("python /home/yeastimages/LOGS3/Scripts/makeHTML_HTS.py",barcode,imtime)
        print(string)
        if(!skipDone|length(dir(file.path("QFA_EXPERIMENTS",barcode,"IMAGEBROWSER")) ==0)){
                system(string)
        }else{
                print(paste("Skipping image browser for",barcode,", already generated"))
        }
  }

  # Clear image file location database, ready to be re-built with latest images
  if(file.exists("barcb.json")) file.remove("barcdb.json")

  for(f in flist){
        print(paste("Making image browsers for",f))
        #makeImBrowser(f,2.0);
        #makeImBrowser(f,0.75);
  }
}
# Merge data from PLOS Genetics screens if any of them have been re-analysed
# Note that this will only happen if the PLOS Genetics experiments are NOT listed as exceptions
if(length(intersect(PLOSGenetics,flist))>0){
        print("Binding PLOS Genetics experiments...")
        source("QFA_EXPERIMENTS/QFA0139/SCRIPTS/QFA0139_Rbind.R")
        source("QFA_EXPERIMENTS/QFA0140/SCRIPTS/QFA0140_rbind.R")
        source("QFA_EXPERIMENTS/QFA0141/SCRIPTS/QFA0141_rbind.R")
}