initial commit

GPS_opt_rep1.r

+
+############
+##########
+#GPS_opt
+#############
+##############
+
+
+##First read in the arguments listed at the command line
+args=(commandArgs(TRUE))
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    #a = 1
+    #b = c(1,1,1)
+    run=1
+    scenario=1
+}else{
+    for(i in 1:length(args)){
+         eval(parse(text=args[[i]]))
+    }
+}
+
+print(paste("run",run))
+print(paste("scenario",scenario))
+
+
+library(Rcpp)
+Sys.setenv("PKG_CXXFLAGS"=paste("-std=c++11 -O3 -I", '/work/sbensadoun/comp_PS_GS/script/sor/stats/include' , sep=""))
+sourceCpp("/work/sbensadoun/comp_PS_GS/script/sor/src/sor.cpp", verbose = T)
+source('/work/sbensadoun/comp_PS_GS/script/sor4.R')
+library(parallel)
+
+
+
+#################
+
+source("/work/sbensadoun/comp_PS_GS/script/function_opt.r")
+library(rrBLUP)
+library(data.table)
+
+ncpu=1
+outdir="/work/sbensadoun/comp_PS_GS/GPS/opt_cross"
+
+geno.file="/work/sbensadoun/comp_PS_GS/donnees_entree/wp4_pheno_prune0.5_01_nohet.txt"
+map.file="/work/sbensadoun/comp_PS_GS/donnees_entree/wp4_pheno_prune0.5_def.map"
+design.file="/work/sbensadoun/comp_PS_GS/donnees_entree/design_190308.txt"
+effect.file=paste("WP4_12K_100effect_run",run,".txt",sep="")
+
+setwd(outdir)
+
+
+design=read.table(design.file,header=T)
+design$strategy="GPS"
+design$crossing="opt"
+
+
+#run=1
+parameter=as.vector(as.matrix(design[scenario,]))
+names(parameter)=colnames(design)
+param.PS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"PS.NC","PS.N2","PS.N3","PS.N4",
+"alpha4PS","alpha3PS","alphaPS",
+"CTPS",
+"PS.n2",
+"PS.n3",
+"PS.n4",
+"years",
+"CTPS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GPS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GPS.NC","GPS.N2","GPS.N3","GPS.N4",
+"alpha4GPS","alpha3GPS","alphaGPS",
+"CTGPS",
+"GPS.n2",
+"GPS.n3",
+"GPS.n4",
+"years",
+"CTGPS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GPS.NC=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GPSn2.NC","GPSn2.N2","GPSn2.N3","GPSn2.N4",
+"alpha4GPSn2","alpha3GPSn2","alphaGPSn2",
+"CTGPSn2",
+"GPSn2.n2",
+"GPSn2.n3",
+"GPSn2.n4",
+"years",
+"CTGPSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GS.NC","GS.N2","GS.N3","GS.N4",
+"alpha4GS","alpha3GS","alphaGS",
+"CTGS",
+"GS.n2",
+"GS.n3",
+"GS.n4",
+"years",
+"CTGS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GS.NC=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GSn2.NC","GSn2.N2","GSn2.N3","GSn2.N4",
+"alpha4GSn2","alpha3GSn2","alphaGSn2",
+"CTGSn2",
+"GSn2.n2",
+"GSn2.n3",
+"GSn2.n4",
+"years",
+"CTGSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+parameter=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","NC","K","CT","CTgs","lambda","alpha2",
+"PS.NC","PS.N2","PS.N3","PS.N4",
+"GPS.NC","GPS.N2","GPS.N3","GPS.N4",
+"GPSn2.NC","GPSn2.N2","GPSn2.N3","GPSn2.N4",
+"GS.NC","GS.N2","GS.N3","GS.N4",
+"GSn2.NC","GSn2.N2","GSn2.N3","GSn2.N4",
+####
+"alpha4GPS","alpha3GPS","alphaGPS",
+"alpha4GPSn2","alpha3GPSn2","alphaGPSn2",
+"alpha4PS","alpha3PS","alphaPS",
+"alpha4GS","alpha3GS","alphaGS",
+"alpha4GSn2","alpha3GSn2","alphaGSn2",
+"CTPS",
+"CTGPS",
+"CTGPSn2",
+"CTGS",
+"CTGSn2",
+"PS.n2",
+"GPS.n2",
+"GPSn2.n2",
+"GS.n2",
+"GSn2.n2",
+"PS.n3",
+"GPS.n3",
+"GPSn2.n3",
+"GS.n3",
+"GSn2.n3",
+"PS.n4",
+"GPS.n4",
+"GPSn2.n4",
+"GS.n4",
+"GSn2.n4",
+"years",
+"years.gs",
+"CTPS.year",
+"CTGPS.year",
+"CTGPSn2.year",
+"CTGS.year",
+"CTGSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param=param.GPS
+names(param)=c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"NC","N2","N3","N4",
+"alpha4","alpha3","alpha",
+"CT",
+"n2",
+"n3",
+"n4",
+"years",
+"CT.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)
+
+
+NC=as.numeric(param["NC"])
+NP=as.numeric(param["NP"])
+K=as.numeric(param["K"])
+N3=as.numeric(param["N3"])
+N4=as.numeric(param["N4"])
+
+
+bycross4=as.numeric(param["bycross4"])
+bycrossp=as.numeric(param["bycrossp"])
+size4=as.numeric(param["size4"])
+sizep=as.numeric(param["sizep"])
+crossing=param["crossing"]
+strategy=param["strategy"]
+h2=as.numeric(param["h2"])
+
+header=paste(strategy,crossing,sep="_")
+header2="rep1_WP4_12K_100QTL"
+
+res=c("strategy","scenario","run","year","CG","K","bycross4","bycrossp","size4","sizep","h2","NC","N2","N3","N4","TBV10","TBV25","TBV50","TBV100","TBV200","rate10","rate25","rate50","rate100","rate200","rate","rateNP10","rateNP25","rateNP50","rateNP100","rateNP200","nbqtl10","nbqtl25","nbqtl50","nbqtl100","nbqtl200","nbal","accu","rmse","var.tbv")
+write.table(t(data.frame(res)),paste(header2,"_",header,"_scenario",scenario,"_run",run,"_stat.txt",sep=""),quote=F,col.names=F,row.names=F,sep="\t")
+
+
+
+####
+
+y=as.numeric(param["years"])
+years=seq(5,y,5)
+maxy=max(years)
+
+effects=as.vector(read.table(effect.file)[,1])
+
+geno2=read.table(geno.file,check.names=F)
+map2=read.table(map.file)
+
+TBV=generate_BV(as.matrix(geno2),effects)
+
+
+geno3=geno2[,effects==0]
+
+map3=map2[effects==0,]
+
+pheno=prod_noise(TBV,h2)
+
+prog=geno2
+
+if (bycross4==0)
+{
+n3s=balance(N3,NC)
+}
+names=1001:(1000+NP)
+prog3=geno3
+names(pheno)=rownames(geno2)
+
+estimated_effects=estimate_effect(pheno,geno3)
+
+map=as.matrix(map2)[,c(1,3)]
+#map[,2]=round(map2[,4]/4000000,2)
+map=apply(map,2,as.numeric)
+map[,2]=round(map[,2],2)
+
+
+
+year=0
+nam=paste(header2,"_",header,"_scenario",scenario,"_run",run,"_year",year,"_",sep="")
+write.table(data.frame(estimated_effects),paste(nam,"_estimated_effects.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+fwrite(data.frame(prog),paste(nam,"_progeny.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+fwrite(data.frame(pheno),paste(nam,"_pheno.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+
+nam2=paste(header2,"_",header,"_scenario",scenario,"_run",run,sep="")
+
+fwrite(data.frame(prog),paste(nam2,"_pro.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+fwrite(data.frame(pheno),paste(nam2,"_pheno.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+
+prog=prog[rev(order(pheno)),]
+pheno=pheno[rev(order(pheno)),]
+prog3=prog[,effects==0]
+
+
+for (i in 1:K){
+
+
+for (j in 1:3){
+	print(i)
+	print(j)
+	#year=(12*(i-1))+(4*j)
+	year=(15*(i-1))+(5*j)
+
+	nam=paste(header2,"_",header,"_scenario",scenario,"_run",run,"_year",year,"_",sep="")
+
+
+	if (crossing=="random")
+	{
+
+	cross=cross_random2(Nind=NP,NC=NC)
+
+	cr=cbind(rownames(prog)[cross[,1]],rownames(prog)[cross[,2]])
+	cross=data.frame(cross)
+
+	}
+
+	if (crossing=="opt")
+	{
+
+	cr=cross_value_best_chr(estimated_effects,as.matrix(prog3),map3)
+
+	print("cr1 ok")
+	cr=as.matrix(cr[1:NC,1:2])
+	cr=apply(cr,2,as.numeric)
+
+	print("cr2 ok")
+	cross=data.frame(cr)
+
+	cr=cbind(rownames(prog)[as.numeric(as.vector(cr[,1]))],rownames(prog)[as.numeric(as.vector(cr[,2]))])
+	}
+
+
+	########
+	data=cbind.data.frame(rownames(prog),prog)
+
+	npro=n3s
+	nam=paste(header2,"_",header,"_scenario",scenario,"_run",run,"_year",year,"_",sep="")
+	filePrefix=nam
+	compressFile=TRUE
+
+	sor_parallel(map, cross, data, filePrefix=nam, compressFile=TRUE, ncpu=ncpu,npro=npro)
+
+	res=vector("list",nrow(cross))
+
+	nam=paste(header2,"_",header,"_scenario",scenario,"_run",run,"_year",year,"_",sep="")
+
+	nam2=paste(nam,as.vector(cross[,1]),"_x_",as.vector(cross[,2]),sep="")
+
+
+	for (l in 1:length(nam2)){
+		#print(l)
+		res[[l]]=sor_read_file(nam2[l])/2
+		}
+
+	file.remove(nam2)
+	##############
+	print("pro ok")
+
+	date()
+	result=cycle_GPS(header2=header2,header=header,year=year,cross=cr,pro.sp=res,parameters=param,scenario=scenario,run=run,estimated_effects=estimated_effects,effects=effects,names=names,n3s=n3s)
+	date()
+
+	print("cycle ok")
+
+	ped=result[[1]]
+	prog=result[[2]]
+	pheno4=result[[3]]
+	prog4=result[[4]]
+
+	nam=paste(header2,"_",header,"_scenario",scenario,"_run",run,"_year",year,"_",sep="")
+	colnames(prog)=as.vector(map2[,2])
+
+	fwrite(data.frame(prog),paste(nam,"_progeny.txt",sep=""),quote=F,row.names=T,col.names=T,sep="\t")
+	fwrite(data.frame(ped),paste(nam,"_pedigree.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+
+	nam2=paste(header2,"_",header,"_scenario",scenario,"_run",run,sep="")
+
+	fwrite(data.frame(prog4),paste(nam2,"_pro.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t",append=T)
+	fwrite(data.frame(pheno4),paste(nam2,"_pheno.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t",append=T)
+
+
+	if (year!=maxy)
+	{
+	names=names+NP
+
+	prog.tmp=fread(paste(nam2,"_pro.txt",sep=""),data.table=F)
+	pheno.tmp=fread(paste(nam2,"_pheno.txt",sep=""),data.table=F)
+
+	estimated_effects=estimate_effect(as.vector(as.matrix(pheno.tmp)),as.matrix(prog.tmp[,effects==0]))
+	write.table(data.frame(estimated_effects),paste(nam,"_estimated_effects.txt",sep=""),quote=F,row.names=F,col.names=F,sep="\t")
+	prog3=prog[,effects==0]
+
+
+
+	print("read ok")
+
+	}
+}
+
+}
+
+

GPS_random_rep1.r

+############
+##########
+#GPS_random
+#############
+##############
+
+
+##First read in the arguments listed at the command line
+args=(commandArgs(TRUE))
+
+##args is now a list of character vectors
+## First check to see if arguments are passed.
+## Then cycle through each element of the list and evaluate the expressions.
+if(length(args)==0){
+    print("No arguments supplied.")
+    ##supply default values
+    #a = 1
+    #b = c(1,1,1)
+    run=1
+    scenario=1
+}else{
+    for(i in 1:length(args)){
+         eval(parse(text=args[[i]]))
+    }
+}
+
+print(paste("run",run))
+print(paste("scenario",scenario))
+
+
+library(Rcpp)
+Sys.setenv("PKG_CXXFLAGS"=paste("-std=c++11 -O3 -I", '/work/sbensadoun/comp_PS_GS/script/sor/stats/include' , sep=""))
+sourceCpp("/work/sbensadoun/comp_PS_GS/script/sor/src/sor.cpp", verbose = T)
+source('/work/sbensadoun/comp_PS_GS/script/sor4.R')
+library(parallel)
+
+
+#################
+
+
+source("/work/sbensadoun/comp_PS_GS/script/function_opt.r")
+library(rrBLUP)
+library(data.table)
+
+ncpu=1
+outdir="/work/sbensadoun/comp_PS_GS/GPS/random"
+
+geno.file="/work/sbensadoun/comp_PS_GS/donnees_entree/wp4_pheno_prune0.5_01_nohet.txt"
+map.file="/work/sbensadoun/comp_PS_GS/donnees_entree/wp4_pheno_prune0.5_def.map"
+design.file="/work/sbensadoun/comp_PS_GS/donnees_entree/design_190308.txt"
+effect.file=paste("WP4_12K_100effect_run",run,".txt",sep="")
+
+
+
+setwd(outdir)
+
+
+design=read.table(design.file,header=T)
+design$strategy="GPS"
+design$crossing="random"
+
+
+#run=1
+parameter=as.vector(as.matrix(design[scenario,]))
+names(parameter)=colnames(design)
+param.PS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"PS.NC","PS.N2","PS.N3","PS.N4",
+"alpha4PS","alpha3PS","alphaPS",
+"CTPS",
+"PS.n2",
+"PS.n3",
+"PS.n4",
+"years",
+"CTPS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GPS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GPS.NC","GPS.N2","GPS.N3","GPS.N4",
+"alpha4GPS","alpha3GPS","alphaGPS",
+"CTGPS",
+"GPS.n2",
+"GPS.n3",
+"GPS.n4",
+"years",
+"CTGPS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GPS.NC=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GPSn2.NC","GPSn2.N2","GPSn2.N3","GPSn2.N4",
+"alpha4GPSn2","alpha3GPSn2","alphaGPSn2",
+"CTGPSn2",
+"GPSn2.n2",
+"GPSn2.n3",
+"GPSn2.n4",
+"years",
+"CTGPSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GS=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GS.NC","GS.N2","GS.N3","GS.N4",
+"alpha4GS","alpha3GS","alphaGS",
+"CTGS",
+"GS.n2",
+"GS.n3",
+"GS.n4",
+"years",
+"CTGS.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+param.GS.NC=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","K","CT","lambda","alpha2",
+"GSn2.NC","GSn2.N2","GSn2.N3","GSn2.N4",
+"alpha4GSn2","alpha3GSn2","alphaGSn2",
+"CTGSn2",
+"GSn2.n2",
+"GSn2.n3",
+"GSn2.n4",
+"years",
+"CTGSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"
+)]
+
+parameter=parameter[c("scenario","CC","CDH","CM2","CM3","CM4","CP3","CP4","CG","Nref","NP","NC","K","CT","CTgs","lambda","alpha2",
+"PS.NC","PS.N2","PS.N3","PS.N4",
+"GPS.NC","GPS.N2","GPS.N3","GPS.N4",
+"GPSn2.NC","GPSn2.N2","GPSn2.N3","GPSn2.N4",
+"GS.NC","GS.N2","GS.N3","GS.N4",
+"GSn2.NC","GSn2.N2","GSn2.N3","GSn2.N4",
+####
+"alpha4GPS","alpha3GPS","alphaGPS",
+"alpha4GPSn2","alpha3GPSn2","alphaGPSn2",
+"alpha4PS","alpha3PS","alphaPS",
+"alpha4GS","alpha3GS","alphaGS",
+"alpha4GSn2","alpha3GSn2","alphaGSn2",
+"CTPS",
+"CTGPS",
+"CTGPSn2",
+"CTGS",
+"CTGSn2",
+"PS.n2",
+"GPS.n2",
+"GPSn2.n2",
+"GS.n2",
+"GSn2.n2",
+"PS.n3",
+"GPS.n3",
+"GPSn2.n3",
+"GS.n3",
+"GSn2.n3",
+"PS.n4",
+"GPS.n4",
+"GPSn2.n4",
+"GS.n4",
+"GSn2.n4",
+"years",
+"years.gs",
+"CTPS.year",
+"CTGPS.year",
+"CTGPSn2.year",
+"CTGS.year",
+"CTGSn2.year",
+"bycross4",
+"bycrossp",
+"size4",
+"sizep",
+"h2",
+"strategy",
+"crossing"