# all txt files should be in a single folder, x = any file in that folder (function reads all of them in the folder)
# it also needs the number of loci
Lmmat <- function(x, loci, all=TRUE){
x <- dirname(x)
xz <- as.vector(list.files(x, pattern='txt'))
x <- file.path(x,list.files(x, pattern='.txt'))
zcc <- list()
if (all==TRUE){
loci2 <- loci + 1
}
else{
loci2 <- loci
}
for (i in seq(1, loci2)){
y <- readLines(x[[i]])
lnum <- grep('Bezier', y)
z <- unlist(strsplit(y[lnum], '[[:blank:]][[:blank:]]'))
zz <- grep('[[:alnum:]]', z, value=TRUE)
zc <- matrix(NA, nrow=length(xz), ncol=length(zz))
rownames(zc) <- xz
colnames(zc) <- zz
if (i==loci+1){
an <- 2
}
else{
an <- 1
}
for (j in seq(1, length(x))){
y <- readLines(x[[j]])
lnum <- grep('Bezier', y)
xa <- unlist(strsplit(y[lnum+an+i], '[[:blank:]]'))
za <- grep('[[:alnum:]]', xa, value=TRUE)
if (i==loci2){
za[[1]] <- loci2
zc[j,] <- as.numeric(za)
}
else{
zc[j,] <- as.numeric(za)
}
}
zcc[[i]] <- zc
}
zcc
}
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