R/run_pipeline.R
In USDA-ARS-GBRU/crossword: Breeding program similation sotware
Defines functions
run_pipeline
Documented in
run_pipeline
run_pipeline <- function(script_file)
{
if(missing(script_file))
{
stop("ERROR: input script file should be provided.")
}
lines = readLines(script_file)
running_script = paste0(script_file,"_running_script.R")
write("##running R script",file=running_script,append=FALSE)
write("library(crossword)",file=running_script,append=TRUE)
test_g2p = FALSE
test_mode = FALSE
for (i in 1:length(lines))
{
line=lines[i]
line = gsub('#.*','',line)
line = gsub(' ','',line)
line = gsub('\t*','',line)
if(line != '')
{
if(grepl("test_mode",line))
{
test_mode = TRUE
}
if(grepl("gff=",line))
{
line = gsub("\"","",gsub("gff=","",line))
line = paste0(input_folder,"/",line)
line = paste0("gff=\"",line,"\"")
}
if(grepl("chr_stat=",line))
{
line = gsub("\"","",gsub("chr_stat=","",line))
line = paste0(input_folder,"/",line)
line = paste0("chr_stat=\"",line,"\"")
}
if(grepl("chr_length=",line))
{
line = gsub("\"","",gsub("chr_length=","",line))
line = paste0(input_folder,"/",line)
line = paste0("chr_length=\"",line,"\"")
}
if(grepl("input=",line))
{
line = gsub("\"","",gsub("input=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input=\"",line,"\"")
}
if(grepl("input_loci=",line))
{
eval(parse(text = line))
if(!(is.na(input_loci)||input_loci==""))
{
line = gsub("\"","",gsub("input_loci=","",line))
line = paste0(input_folder,"/",line)
line = paste0("gen2phy=\"",line,"\"")
test_g2p = TRUE
}
}
if(grepl("input_pheno=",line))
{
line = gsub("\"","",gsub("input_pheno=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input_pheno=\"",line,"\"")
}
if(grepl("input_effects=",line))
{
line = gsub("\"","",gsub("input_effects=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input_effects=\"",line,"\"")
}
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
if (strsplit(line,"")[[1]][1] == "I")
{
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
print("header was read")
write("dir.create(output_folder)",file=running_script,append=TRUE)
dir.create(output_folder)
if(test_g2p==FALSE)
{
write("gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)",file=running_script,append=TRUE)
write("draw_PGplots(gen2phy,paste0(output_folder,\"/gen2phy_graphs\"),im_type)",file=running_script,append=TRUE)
write("parental_genotypes = get_parental_genotypes(input,gen2phy,homo) ",file=running_script,append=TRUE)
write("genotypes_out(parental_genotypes,paste0(output_folder,\"/parental_genotypes\"))",file=running_script,append=TRUE)
gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)
draw_PGplots(gen2phy,paste0(output_folder,"/gen2phy_graphs"),im_type)
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
genotypes_out(parental_genotypes,paste0(output_folder,"/parental_genotypes"))
suppressWarnings(dput(gen2phy,file=paste0(output_folder,"/parental_genotypes_gen2phy_info"),control = "all"))
print("parental_genotypes were obtained")
}else #if a recombination map is supplied (ex. "map.loc"), then expensive gff compute can be skipped.
{
write("parental_genotypes = get_parental_genotypes(input,gen2phy,homo)",file=running_script,append=TRUE)
#write("gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)",file=running_script,append=TRUE)
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
#gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)
}
break
}
}
}
for (l in 1:iterations)
{
if(test_mode == TRUE){set.seed(l)}
write("###############################################",file=running_script,append=TRUE)
write(paste0("###iteration# ",l,"################################"),file=running_script,append=TRUE)
write(paste0("l=",l),file=running_script,append=TRUE)
write("dir.create(paste0(output_folder,\"/iteration_\",l))",file=running_script,append=TRUE)
dir.create(paste0(output_folder,"/iteration_",l))
tgv_only = FALSE
PHENO = list()
PHENO[["test"]] = NA
########getting phenotyping method
if(phenotyping_method == "QTN_random")
{
write("qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution)",file=running_script,append=TRUE)
qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution)
}else if(phenotyping_method == "high_low_parents")
{
write("qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution,highest_P=highest_P,lowest_P=lowest_P,high_to_low_percentage=high_to_low_percentage)",file=running_script,append=TRUE)
qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution,highest_P=highest_P,lowest_P=lowest_P,high_to_low_percentage=high_to_low_percentage)
}else if(phenotyping_method =="QTN_supplied")
{
write("qtn_effect = read.table(input_effects)",file=running_script,append=TRUE)
write("colnames(qtn_effect) = c(\"QTN\",\"ref\",\"effect\")",file=running_script,append=TRUE)
write("rownames(qtn_effect) = qtn_effect$QTN",file=running_script,append=TRUE)
qtn_effect = read.table(input_effects)
colnames(qtn_effect) = c("QTN","ref","effect")
rownames(qtn_effect) = qtn_effect$QTN
}
######getting heritability mode
if(heritability_mode == "absolute")
{
write("vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode=\"absolute\")",file=running_script,append=TRUE)
vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode="absolute")
}else if(heritability_mode == "average")
{
write("vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode=\"average\")",file=running_script,append=TRUE)
vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode="average")
}
write("loci = parental_genotypes[[2]][as.character(qtn_effect$QTN),]",file=running_script,append=TRUE)
loci = parental_genotypes[[2]][as.character(qtn_effect$QTN),]
write("write.table(cbind(qtn_effect,loci),paste0(output_folder,\"/iteration_\",l,\"/selected_QTNs\"),col.names=TRUE,row.names=FALSE,quote =FALSE)",file=running_script,append=TRUE)
write.table(cbind(qtn_effect,loci),paste0(output_folder,"/iteration_",l,"/selected_QTNs"),col.names=TRUE,row.names=FALSE,quote =FALSE)
for (i in 1:length(lines))
{
line=lines[i]
line = gsub('#.*','',line)
line = gsub(' ','',line)
line = gsub('\t*','',line)
if(line != '')
{
if(grepl("=cross",line))
{
pop=sub("(.*)=cross.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length,parental_genotypes=parental_genotypes,isdh=FALSE)",line)
Line=gsub("=cross","=crossword::cross",Line)
Line=gsub("list[(]","c(",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=advance",line))
{
pop=sub("(.*)=advance.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length)",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=create_families",line))
{
pop=sub("(.*)=create_families.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length)",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=pick_individual",line))
{
pop=sub("(.*)=pick_individual.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: individual ",pop," was picked"))
}
if(grepl("haplotypes_out",line))
{
Line = gsub("output=\"",paste0("output=\"",output_folder,"/iteration_",l,"/"),line)
Line = gsub(")$",paste0(",parental_genotypes=parental_genotypes)"),Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",gsub(".*pop=(.*),output.*","\\1",Line)," was exported"))
}
if(grepl("=haplotypes_in",line))
{
Line = gsub("=\"",paste0("=\"",output_folder,"/iteration_",l,"/"),line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: individual ",sub("(.*)=haplotypes_in.*","\\",Line)," was imported"))
}
if(grepl("=combine_populations",line))
{
Line = gsub("list[(]","c(",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: pupulations were combined"))
}
###########################phenotyping:get_phenotype/select/reduce##################
if(grepl("=select[(]",line) || grepl("=get_phenotype",line))
{
if(grepl("tgv_only=TRUE",line))
{
tgv_only = TRUE
}else
{
tgv_only = FALSE
}
c1 = sub("(^.*)=.*[(].*$","\\1",line)
c2 = sub(".*pop=(.*)[,][Nt].*","\\1",line)
if(grepl("phenotype=NA",line) || grepl("phenotype=\"\"",line))
{
line = gsub(",phenotype=.*)",")",line)
}
if(length(names(PHENO)[which(names(PHENO) %in% c2)]) == 1)
{
pheno = PHENO[[c2]]
}else if (grepl("phenotype=",line))
{
com1 = sub(".*phenotype(=.*)[)]","\\1",line)
write(paste0("pheno", com1),file=running_script,append=TRUE)
eval(parse(text = paste0("pheno", com1)))
line = gsub(",phenotype=.*)",")",line)
}else
{
com1 = paste0("pheno = phenotype(pop=",c2,",qtn_effect=qtn_effect,tgv_only=",tgv_only,",vr=vr,parental_genotypes=parental_genotypes)")
write(com1,file=running_script,append=TRUE)
eval(parse(text = com1))
PHENO[[c2]] = pheno
}
line = gsub(",phenotype=.*)",")",line)
if(grepl("=get_phenotype",line))
{
write(paste0(c1," = pheno"),file=running_script,append=TRUE)
eval(parse(text = paste0(c1," = pheno")))
print(paste0("Iteration_",l," #########processed: phenotyping was calculated"))
}else if(grepl("=select",line))
{
if(grepl("%",line))
{
percentage=TRUE
write("percentage=TRUE",file=running_script,append=TRUE)
}else
{
percentage=FALSE
write("percentage=FALSE",file=running_script,append=TRUE)
}
Line = gsub("%","",line)
sub0 = paste0("pop=",c2,",")
sub1 = sub(".*,(N.*)[)]","\\1",Line)
file_path = paste0(output_folder,"/iteration_",l,"/",c2)
sub2 = paste0(",pheno=pheno,percentage=percentage,im_type=im_type,file=\"",file_path,"\")")
com2 = paste0(c1,"=select(",sub0,sub1,sub2)
write(com2,file=running_script,append=TRUE)
eval(parse(text = com2))
print(paste0("Iteration_",l," #########processed: a sub population was created based on selection"))
}
tgv_only <<- FALSE
}
if(grepl("=dh",line))
{
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
print(paste0("Iteration_",l," #########processed: double haploid process was done"))
}
if(grepl("draw_haplotypes",line))
{
Line = line
pop = sub(".*=(.*)[)]","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
ss = paste0(output_folder,"/iteration_",l,"/",pop)
write(paste0("ss=\"",ss,"\""),file=running_script,append=TRUE)
Line = gsub(")",",output_folder=ss,parental_genotypes=parental_genotypes,heterozygous=heterozygous,by_chromosomes=by_chromosomes,im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," haplotypes were created"))
}
if(grepl("draw_population",line))
{
Line = line
pop = sub(".*[(]pop=(.*)[)]","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
ss = paste0(output_folder,"/iteration_",l,"/",pop,"_plots")
write(paste0("ss=\"",ss,"\""),file=running_script,append=TRUE)
Line = gsub(")",",file=ss,parental_genotypes=parental_genotypes,im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," graphs were created"))
}
if (grepl("get_genotypes",line))
{
Line = gsub("get_genotypes[(]","get_genotypes(parental_genotypes=parental_genotypes,",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genotypes were rerieved"))
}
if (grepl("create_marker_set",line))
{
Line = line
if(grepl("no_qtn=FALSE",Line))
{
Line = gsub(",no_qtn=FALSE","",Line)
}else if(grepl("no_qtn=TRUE",Line))
{
Line = gsub("no_qtn=TRUE","no_qtn=as.character(qtn_effect$QTN)",Line)
}
if(grepl("biased_selection=TRUE",Line))
{
Line = gsub("[)]$",",gen2phy=gen2phy,parental_genotypes=parental_genotypes)",Line)
}
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: the marker set was created"))
}
if (grepl("genomic_prediction",line))
{
Line = line
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genomic prediction was applied"))
}
if (grepl("genotypes_out",line))
{
Line = line
file_path = paste0(output_folder,"/iteration_",l)
Line = gsub("output=\"",paste0("output=\"",file_path,"/"),Line)
Line = gsub("[)]$",",parental_genotypes=parental_genotypes)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genotypes were exported"))
}
if (grepl("phenotype_out",line))
{
Line = line
ss = sub(".*file=\"(.*)\",level.*","\\1",Line)
ss = paste0(output_folder,"/iteration_",l,"/",ss)
ss2 = paste0(gsub(".*(,level.*)[)]","\\1",line),",N=100,method=\"top\",percentage=TRUE)")
Line = gsub("file=.*[)]",paste0("file=\"",ss,"\")") ,Line)
Line=gsub("[)]",",im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
file_path = paste0(output_folder,"/iteration_",l)
Line2 = gsub("file=.*,im_type",paste0("file=\"",ss,"\",im_type"),Line)
invisible(eval(parse(text = gsub("phenotype_out","select",gsub(")",ss2,Line2)))))
print(paste0("Iteration_",l," #########processed: the phenotypes were exported"))
}
if (grepl("=mas",line))
{
Line = line
ss = sub(".*([[].*[]]).*","\\1",Line)
ss2 = gsub("[]]",")",gsub("[)],[(]","),c(",gsub("[[]","list(c",ss)))
Line = gsub("[[].*[]]",ss2,Line)
Line = gsub(")$",",parental_genotypes=parental_genotypes)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: MAS was applied"))
}
if (grepl("create_population",line))
{
pop = strsplit(line,'=')[[1]][1]
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub("@","",line)
Line = gsub("P=","",Line)
pop=sub("(^.*)=.*","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",chr_length=chr_length,parental_genotypes=parental_genotypes)",Line)
Line=gsub("list[(]","c(",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
}
}
invisible(gc())
}
}
USDA-ARS-GBRU/crossword documentation built on April 5, 2023, 7:29 p.m.
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Defines functions run_pipeline
Documented in run_pipeline
run_pipeline <- function(script_file)
{
if(missing(script_file))
{
stop("ERROR: input script file should be provided.")
}
lines = readLines(script_file)
running_script = paste0(script_file,"_running_script.R")
write("##running R script",file=running_script,append=FALSE)
write("library(crossword)",file=running_script,append=TRUE)
test_g2p = FALSE
test_mode = FALSE
for (i in 1:length(lines))
{
line=lines[i]
line = gsub('#.*','',line)
line = gsub(' ','',line)
line = gsub('\t*','',line)
if(line != '')
{
if(grepl("test_mode",line))
{
test_mode = TRUE
}
if(grepl("gff=",line))
{
line = gsub("\"","",gsub("gff=","",line))
line = paste0(input_folder,"/",line)
line = paste0("gff=\"",line,"\"")
}
if(grepl("chr_stat=",line))
{
line = gsub("\"","",gsub("chr_stat=","",line))
line = paste0(input_folder,"/",line)
line = paste0("chr_stat=\"",line,"\"")
}
if(grepl("chr_length=",line))
{
line = gsub("\"","",gsub("chr_length=","",line))
line = paste0(input_folder,"/",line)
line = paste0("chr_length=\"",line,"\"")
}
if(grepl("input=",line))
{
line = gsub("\"","",gsub("input=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input=\"",line,"\"")
}
if(grepl("input_loci=",line))
{
eval(parse(text = line))
if(!(is.na(input_loci)||input_loci==""))
{
line = gsub("\"","",gsub("input_loci=","",line))
line = paste0(input_folder,"/",line)
line = paste0("gen2phy=\"",line,"\"")
test_g2p = TRUE
}
}
if(grepl("input_pheno=",line))
{
line = gsub("\"","",gsub("input_pheno=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input_pheno=\"",line,"\"")
}
if(grepl("input_effects=",line))
{
line = gsub("\"","",gsub("input_effects=","",line))
line = paste0(input_folder,"/",line)
line = paste0("input_effects=\"",line,"\"")
}
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
if (strsplit(line,"")[[1]][1] == "I")
{
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
print("header was read")
write("dir.create(output_folder)",file=running_script,append=TRUE)
dir.create(output_folder)
if(test_g2p==FALSE)
{
write("gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)",file=running_script,append=TRUE)
write("draw_PGplots(gen2phy,paste0(output_folder,\"/gen2phy_graphs\"),im_type)",file=running_script,append=TRUE)
write("parental_genotypes = get_parental_genotypes(input,gen2phy,homo) ",file=running_script,append=TRUE)
write("genotypes_out(parental_genotypes,paste0(output_folder,\"/parental_genotypes\"))",file=running_script,append=TRUE)
gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)
draw_PGplots(gen2phy,paste0(output_folder,"/gen2phy_graphs"),im_type)
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
genotypes_out(parental_genotypes,paste0(output_folder,"/parental_genotypes"))
suppressWarnings(dput(gen2phy,file=paste0(output_folder,"/parental_genotypes_gen2phy_info"),control = "all"))
print("parental_genotypes were obtained")
}else #if a recombination map is supplied (ex. "map.loc"), then expensive gff compute can be skipped.
{
write("parental_genotypes = get_parental_genotypes(input,gen2phy,homo)",file=running_script,append=TRUE)
#write("gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)",file=running_script,append=TRUE)
parental_genotypes = get_parental_genotypes(input,gen2phy,homo)
#gen2phy = physical2genomic(gff,chr_stat,chr_length,window_size)
}
break
}
}
}
for (l in 1:iterations)
{
if(test_mode == TRUE){set.seed(l)}
write("###############################################",file=running_script,append=TRUE)
write(paste0("###iteration# ",l,"################################"),file=running_script,append=TRUE)
write(paste0("l=",l),file=running_script,append=TRUE)
write("dir.create(paste0(output_folder,\"/iteration_\",l))",file=running_script,append=TRUE)
dir.create(paste0(output_folder,"/iteration_",l))
tgv_only = FALSE
PHENO = list()
PHENO[["test"]] = NA
########getting phenotyping method
if(phenotyping_method == "QTN_random")
{
write("qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution)",file=running_script,append=TRUE)
qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution)
}else if(phenotyping_method == "high_low_parents")
{
write("qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution,highest_P=highest_P,lowest_P=lowest_P,high_to_low_percentage=high_to_low_percentage)",file=running_script,append=TRUE)
qtn_effect = random_qtn_assign(qtn = qtn,gen2phy=gen2phy,biased_selection=biased_selection,parental_genotypes=parental_genotypes,min_qtn_freq=min_qtn_freq,dominant=dominant,effect_distribution=effect_distribution,highest_P=highest_P,lowest_P=lowest_P,high_to_low_percentage=high_to_low_percentage)
}else if(phenotyping_method =="QTN_supplied")
{
write("qtn_effect = read.table(input_effects)",file=running_script,append=TRUE)
write("colnames(qtn_effect) = c(\"QTN\",\"ref\",\"effect\")",file=running_script,append=TRUE)
write("rownames(qtn_effect) = qtn_effect$QTN",file=running_script,append=TRUE)
qtn_effect = read.table(input_effects)
colnames(qtn_effect) = c("QTN","ref","effect")
rownames(qtn_effect) = qtn_effect$QTN
}
######getting heritability mode
if(heritability_mode == "absolute")
{
write("vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode=\"absolute\")",file=running_script,append=TRUE)
vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode="absolute")
}else if(heritability_mode == "average")
{
write("vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode=\"average\")",file=running_script,append=TRUE)
vr = get_vr(qtn_effect = qtn_effect,h2 = h2 ,parental_genotypes=parental_genotypes,dominant=dominant,heritability_mode="average")
}
write("loci = parental_genotypes[[2]][as.character(qtn_effect$QTN),]",file=running_script,append=TRUE)
loci = parental_genotypes[[2]][as.character(qtn_effect$QTN),]
write("write.table(cbind(qtn_effect,loci),paste0(output_folder,\"/iteration_\",l,\"/selected_QTNs\"),col.names=TRUE,row.names=FALSE,quote =FALSE)",file=running_script,append=TRUE)
write.table(cbind(qtn_effect,loci),paste0(output_folder,"/iteration_",l,"/selected_QTNs"),col.names=TRUE,row.names=FALSE,quote =FALSE)
for (i in 1:length(lines))
{
line=lines[i]
line = gsub('#.*','',line)
line = gsub(' ','',line)
line = gsub('\t*','',line)
if(line != '')
{
if(grepl("=cross",line))
{
pop=sub("(.*)=cross.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length,parental_genotypes=parental_genotypes,isdh=FALSE)",line)
Line=gsub("=cross","=crossword::cross",Line)
Line=gsub("list[(]","c(",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=advance",line))
{
pop=sub("(.*)=advance.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length)",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=create_families",line))
{
pop=sub("(.*)=create_families.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",id=pop,chr_length=chr_length)",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
if(grepl("=pick_individual",line))
{
pop=sub("(.*)=pick_individual.*","\\1",line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: individual ",pop," was picked"))
}
if(grepl("haplotypes_out",line))
{
Line = gsub("output=\"",paste0("output=\"",output_folder,"/iteration_",l,"/"),line)
Line = gsub(")$",paste0(",parental_genotypes=parental_genotypes)"),Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",gsub(".*pop=(.*),output.*","\\1",Line)," was exported"))
}
if(grepl("=haplotypes_in",line))
{
Line = gsub("=\"",paste0("=\"",output_folder,"/iteration_",l,"/"),line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: individual ",sub("(.*)=haplotypes_in.*","\\",Line)," was imported"))
}
if(grepl("=combine_populations",line))
{
Line = gsub("list[(]","c(",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: pupulations were combined"))
}
###########################phenotyping:get_phenotype/select/reduce##################
if(grepl("=select[(]",line) || grepl("=get_phenotype",line))
{
if(grepl("tgv_only=TRUE",line))
{
tgv_only = TRUE
}else
{
tgv_only = FALSE
}
c1 = sub("(^.*)=.*[(].*$","\\1",line)
c2 = sub(".*pop=(.*)[,][Nt].*","\\1",line)
if(grepl("phenotype=NA",line) || grepl("phenotype=\"\"",line))
{
line = gsub(",phenotype=.*)",")",line)
}
if(length(names(PHENO)[which(names(PHENO) %in% c2)]) == 1)
{
pheno = PHENO[[c2]]
}else if (grepl("phenotype=",line))
{
com1 = sub(".*phenotype(=.*)[)]","\\1",line)
write(paste0("pheno", com1),file=running_script,append=TRUE)
eval(parse(text = paste0("pheno", com1)))
line = gsub(",phenotype=.*)",")",line)
}else
{
com1 = paste0("pheno = phenotype(pop=",c2,",qtn_effect=qtn_effect,tgv_only=",tgv_only,",vr=vr,parental_genotypes=parental_genotypes)")
write(com1,file=running_script,append=TRUE)
eval(parse(text = com1))
PHENO[[c2]] = pheno
}
line = gsub(",phenotype=.*)",")",line)
if(grepl("=get_phenotype",line))
{
write(paste0(c1," = pheno"),file=running_script,append=TRUE)
eval(parse(text = paste0(c1," = pheno")))
print(paste0("Iteration_",l," #########processed: phenotyping was calculated"))
}else if(grepl("=select",line))
{
if(grepl("%",line))
{
percentage=TRUE
write("percentage=TRUE",file=running_script,append=TRUE)
}else
{
percentage=FALSE
write("percentage=FALSE",file=running_script,append=TRUE)
}
Line = gsub("%","",line)
sub0 = paste0("pop=",c2,",")
sub1 = sub(".*,(N.*)[)]","\\1",Line)
file_path = paste0(output_folder,"/iteration_",l,"/",c2)
sub2 = paste0(",pheno=pheno,percentage=percentage,im_type=im_type,file=\"",file_path,"\")")
com2 = paste0(c1,"=select(",sub0,sub1,sub2)
write(com2,file=running_script,append=TRUE)
eval(parse(text = com2))
print(paste0("Iteration_",l," #########processed: a sub population was created based on selection"))
}
tgv_only <<- FALSE
}
if(grepl("=dh",line))
{
write(line,file=running_script,append=TRUE)
eval(parse(text = line))
print(paste0("Iteration_",l," #########processed: double haploid process was done"))
}
if(grepl("draw_haplotypes",line))
{
Line = line
pop = sub(".*=(.*)[)]","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
ss = paste0(output_folder,"/iteration_",l,"/",pop)
write(paste0("ss=\"",ss,"\""),file=running_script,append=TRUE)
Line = gsub(")",",output_folder=ss,parental_genotypes=parental_genotypes,heterozygous=heterozygous,by_chromosomes=by_chromosomes,im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," haplotypes were created"))
}
if(grepl("draw_population",line))
{
Line = line
pop = sub(".*[(]pop=(.*)[)]","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
ss = paste0(output_folder,"/iteration_",l,"/",pop,"_plots")
write(paste0("ss=\"",ss,"\""),file=running_script,append=TRUE)
Line = gsub(")",",file=ss,parental_genotypes=parental_genotypes,im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," graphs were created"))
}
if (grepl("get_genotypes",line))
{
Line = gsub("get_genotypes[(]","get_genotypes(parental_genotypes=parental_genotypes,",line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genotypes were rerieved"))
}
if (grepl("create_marker_set",line))
{
Line = line
if(grepl("no_qtn=FALSE",Line))
{
Line = gsub(",no_qtn=FALSE","",Line)
}else if(grepl("no_qtn=TRUE",Line))
{
Line = gsub("no_qtn=TRUE","no_qtn=as.character(qtn_effect$QTN)",Line)
}
if(grepl("biased_selection=TRUE",Line))
{
Line = gsub("[)]$",",gen2phy=gen2phy,parental_genotypes=parental_genotypes)",Line)
}
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: the marker set was created"))
}
if (grepl("genomic_prediction",line))
{
Line = line
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genomic prediction was applied"))
}
if (grepl("genotypes_out",line))
{
Line = line
file_path = paste0(output_folder,"/iteration_",l)
Line = gsub("output=\"",paste0("output=\"",file_path,"/"),Line)
Line = gsub("[)]$",",parental_genotypes=parental_genotypes)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: genotypes were exported"))
}
if (grepl("phenotype_out",line))
{
Line = line
ss = sub(".*file=\"(.*)\",level.*","\\1",Line)
ss = paste0(output_folder,"/iteration_",l,"/",ss)
ss2 = paste0(gsub(".*(,level.*)[)]","\\1",line),",N=100,method=\"top\",percentage=TRUE)")
Line = gsub("file=.*[)]",paste0("file=\"",ss,"\")") ,Line)
Line=gsub("[)]",",im_type=im_type)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
file_path = paste0(output_folder,"/iteration_",l)
Line2 = gsub("file=.*,im_type",paste0("file=\"",ss,"\",im_type"),Line)
invisible(eval(parse(text = gsub("phenotype_out","select",gsub(")",ss2,Line2)))))
print(paste0("Iteration_",l," #########processed: the phenotypes were exported"))
}
if (grepl("=mas",line))
{
Line = line
ss = sub(".*([[].*[]]).*","\\1",Line)
ss2 = gsub("[]]",")",gsub("[)],[(]","),c(",gsub("[[]","list(c",ss)))
Line = gsub("[[].*[]]",ss2,Line)
Line = gsub(")$",",parental_genotypes=parental_genotypes)",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: MAS was applied"))
}
if (grepl("create_population",line))
{
pop = strsplit(line,'=')[[1]][1]
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub("@","",line)
Line = gsub("P=","",Line)
pop=sub("(^.*)=.*","\\1",Line)
write(paste0("pop=\"",pop,"\""),file=running_script,append=TRUE)
Line = gsub(")$",",chr_length=chr_length,parental_genotypes=parental_genotypes)",Line)
Line=gsub("list[(]","c(",Line)
write(Line,file=running_script,append=TRUE)
eval(parse(text = Line))
print(paste0("Iteration_",l," #########processed: ",pop," was created"))
}
}
}
invisible(gc())
}
}
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