Nothing
PLINKConversion <- function(file.list="", file.path="", output.type="PED/MAP",
job.name=NULL, shared.username=NULL,
print.curl=FALSE, suppress.Warnings=FALSE,
out.basename=NULL) {
output.type <- match.arg(output.type, c("PED/MAP", "TFAM/TPED", "BED/FAM/BIM", "LGEN", "RAWa", "RAWad", "PED/MAP-1/2", "FASTPHASE", "BIMBAM", "STRUCTURE"))
# privAPP=TRUE
# version="plinkconv-beta-1.07"
privAPP=FALSE
version="PLINKconv-hpc-1.07u1"
input.len <- length(file.list)
input.list <- list()
if ((input.len) == 3){
ext1 <- unlist(strsplit(file.list[[1]], "\\."))[2]
ext2 <- unlist(strsplit(file.list[[2]], "\\."))[2]
ext3 <- unlist(strsplit(file.list[[3]], "\\."))[2]
input.type="B"
input.list[[1]] <- find.input(ext1)
input.list[[2]] <- find.input(ext2)
input.list[[3]] <- find.input(ext3)
} else {
ext1 <- unlist(strsplit(file.list[[1]], "\\."))[2]
ext2 <- unlist(strsplit(file.list[[2]], "\\."))[2]
input.list[[1]] <- find.input(ext1)
input.list[[2]] <- find.input(ext2)
if ((ext1 == "tfam" ) || (ext1 == "tped")) {
input.type="T"
} else {
input.type="R"
}
}
if (output.type == "PED/MAP") {
type = "--recode"
} else if (output.type == "TFAM/TPED") {
type = "--recode --transpose"
} else if (output.type == "BED/FAM/BIM") {
type = "--make-bed"
} else if (output.type == "LGEN") {
type = "--recode-lgen"
} else if (output.type == "RAWa") {
type = "--recodeA"
} else if (output.type == "RAWad") {
type = "--recodeAD"
} else if (output.type == "PED/MAP-1/2") {
type = "--recode12"
} else if (output.type == "FASTPHASE") {
type = "--recode-fastphase"
} else if (output.type == "BIMBAM") {
type = "--recode-bimbam"
} else {
type = "--recode-structure"
}
if (input.type=="T"){
options <- list(c("T",TRUE))
if (is.null(out.basename)){
BASE1 <- substr(file.list[[1]],1,nchar(file.list[[1]])-5)
EXT1 <- substr(file.list[[1]],nchar(file.list[[1]])-3,nchar(file.list[[1]]))
BASE2 <- substr(file.list[[2]],1,nchar(file.list[[2]])-5)
if (EXT1 == "tfam"){
out.basename <- paste(BASE1,"_",BASE2, sep="")
} else {
out.basename <- paste(BASE2,"_",BASE1, sep="")
}
}
} else if (input.type=="B") {
options <- list(c("B",TRUE))
if (is.null(out.basename)){
BASE1 <- substr(file.list[[1]],1,nchar(file.list[[1]])-4)
EXT1 <- substr(file.list[[1]],nchar(file.list[[1]])-2,nchar(file.list[[1]]))
BASE2 <- substr(file.list[[2]],1,nchar(file.list[[2]])-4)
EXT2 <- substr(file.list[[2]],nchar(file.list[[2]])-2,nchar(file.list[[1]]))
BASE3 <- substr(file.list[[3]],1,nchar(file.list[[3]])-4)
EXT3 <- substr(file.list[[3]],nchar(file.list[[3]])-2,nchar(file.list[[1]]))
if (EXT1 == "bed" && EXT3 == "bam"){
out.basename <- paste(BASE1, "_", BASE3, "_", BASE2, sep="")
} else if (EXT1 == "bed" && EXT2 == "bam") {
out.basename <- paste(BASE1, "_", BASE2, "_", BASE3, sep="")
} else if (EXT2 == "bed" && EXT3 == "bam"){
out.basename <- paste(BASE2, "_", BASE3, "_", BASE1, sep="")
} else if (EXT3 == "bed" && EXT1 == "bam"){
out.basename <- paste(BASE3, "_", BASE1, "_", BASE2, sep="")
} else if (EXT2 == "bed" && EXT1 == "bam") {
out.basename <- paste(BASE2, "_", BASE1, "_", BASE3, sep="")
} else {
out.basename <- paste(BASE3, "_", BASE2, "_", BASE1, sep="")
}
}
} else {
options <- NULL
if (is.null(out.basename)){
BASE1 <- substr(file.list[[1]],1,nchar(file.list[[1]])-4)
EXT1 <- substr(file.list[[1]],nchar(file.list[[1]])-2,nchar(file.list[[1]]))
BASE2 <- substr(file.list[[2]],1,nchar(file.list[[2]])-4)
if (EXT1 == "map"){
out.basename <- paste(BASE1,"_",BASE2,"_", sep="")
} else {
out.basename <- paste(BASE2,"_",BASE1,"_", sep="")
}
}
}
if (is.null(options)) {
options <- list(c("format", type))
} else {
options <- append(options, list(c("format", type)))
}
options <- append(options, list(c("inputOUT", out.basename)))
if (is.null(job.name)){
job.name <- out.basename
}
# Submit
myJob<-SubmitJob(application=version, args.list=options, job.name=job.name,
file.list=file.list, file.path=file.path,
input.list=input.list, suppress.Warnings=suppress.Warnings,
shared.username=shared.username, print.curl=print.curl,
private.APP=privAPP)
return(myJob)
}
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