#' parse_map: Parse map from CriMAP map output
#' @param mapfile File with output from map
#' @export
parse_map <- function(mapfile){
x <- readLines(mapfile)
map1 <- x[grep("Sex_averaged map", x):(grep("Sex-specific map", x)-1)]
map1 <- map1[3:length(map1)]
map1 <- map1[-which(map1 == "")]
map1 <- map1[1:(length(map1)-2)]
map1 <- data.frame(map1, stringsAsFactors=F)
map1$map2 <- NA
for(i in seq(1, nrow(map1), 2)) map1$map2[i] <- map1$map1[i+1]
map1 <- map1[seq(1, nrow(map1), 2),]
for(i in 1:1e4) if(length(grep(" ", map1$map1) > 0)) map1$map1 <- gsub(" ", " ", map1$map1) else break
for(i in 1:1e4) if(length(grep(" ", map1$map2) > 0)) map1$map2 <- gsub(" ", " ", map1$map2) else break
map <- x[grep("Sex-specific map", x):length(x)]
map <- map[3:length(map)]
map <- map[1:(length(map)-7)]
map <- map[-which(map == "")]
map <- data.frame(map, stringsAsFactors=F)
map$map2 <- NA
for(i in seq(1, nrow(map), 2)) map$map2[i] <- map$map[i+1]
map <- map[seq(1, nrow(map), 2),]
for(i in 1:1e4) if(length(grep(" ", map$map) > 0)) map$map <- gsub(" ", " ", map$map) else break
for(i in 1:1e4) if(length(grep(" ", map$map2) > 0)) map$map2 <- gsub(" ", " ", map$map2) else break
map$Order <- NA
map$SNP.Name <- NA
map$cMPosition.Female <- NA
map$cMPosition.Male <- NA
map$Female.r <- NA
map$cMdiff.Female <- NA
map$Male.r <- NA
map$cMdiff.Male <- NA
map$cMPosition <- NA
map$r <- NA
map$cMdiff <- NA
rm(x)
for(i in 1:nrow(map)){
x <- strsplit(map$map[i], split = " ")[[1]]
if(length(-which(x == "")) > 0) x <- x[-which(x == "")]
x1 <- strsplit(map1$map1[i], split = " ")[[1]]
if(length(-which(x1 == "")) > 0) x1 <- x1[-which(x1 == "")]
map$Order[i] <- x[1]
map$SNP.Name[i] <- x[2]
map$cMPosition.Female[i] <- x[3]
map$cMPosition.Male[i] <- x[4]
map$cMPosition[i] <- x1[3]
rm(x, x1)
x <- strsplit(map$map2[i], split = " ")[[1]]
if(length(-which(x == "")) > 0) x <- x[-which(x == "")]
x1 <- strsplit(map1$map2[i], split = " ")[[1]]
if(length(-which(x1 == "")) > 0) x1 <- x1[-which(x1 == "")]
map$Female.r[i] <- x[1]
map$cMdiff.Female[i] <- x[2]
map$Male.r[i] <- x[3]
map$cMdiff.Male[i] <- x[4]
map$r[i] <- x1[1]
map$cMdiff[i] <- x1[2]
rm(x, x1)
}
map <- subset(map, select = -c(map, map2))
analysisID.val <- gsub("\\\\", "/", mapfile)
analysisID.val <- strsplit(analysisID.val, split = "/")[[1]]
analysisID.val <- analysisID.val[length(analysisID.val)]
analysisID.val <- gsub("chr", "", analysisID.val)
analysisID.val <- gsub(".map", "", analysisID.val, fixed = T)
map$analysisID <- analysisID.val
convert.cols <- which(names(map) %in%
c("Order", "cMPosition.Female", "cMPosition.Male",
"Female.r", "cMdiff.Female", "Male.r", "cMdiff.Male",
"cMPosition", "r", "cMdiff"))
map[,convert.cols] <- sapply(map[,convert.cols], as.numeric)
map
}
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