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### Read FASTA file.
### Return a list contains
### nseq: Number of sequence.
### seqlen: Sequence length.
### seqname: Sequence's name.
### org: Original sequence in nid. array[nsite, nseq]
read.fasta.format <- function(filename, byrow = TRUE, aligned = TRUE,
sep = ""){
ret <- list(code.type = "UNKNOWN", info = NULL, nseq = NULL,
seqlen = NULL, seqname = NULL, org.code = NULL, org = NULL,
byrow = byrow, aligned = aligned)
tmp <- readLines(filename)
tmp.org <- NULL
seqname <- NULL
### parse data.
i <- 1
nseq <- 0
tmp.i <- NULL
repeat{
if(regexpr("^>", tmp[i]) == 1){
if(!is.null(tmp.i)){
# ret$org.code[[nseq]] <- unlist(strsplit(tmp.org, sep))
ret$org.code[[nseq]] <- unlist(strsplit(tmp[tmp.i], sep))
tmp.i <- NULL
}
if(regexpr("\\|", tmp[i]) == 1){
tmp.seqname <- unlist(strsplit(tmp[i], "\\|"))[1]
seqname <- c(seqname, gsub(">(.*)", "\\1", tmp.seqname))
} else{
tmp.seqname <- unlist(strsplit(tmp[i], " "))
tmp.id <- which(nchar(tmp.seqname) > 1)[1]
if(tmp.id == 1){
seqname <- c(seqname, gsub(">(.*)", "\\1", tmp.seqname[tmp.id]))
} else{
seqname <- c(seqname, tmp.seqname[tmp.id])
}
}
nseq <- nseq + 1
} else if(tmp[i] %in% c("", " ")){
} else{
tmp.i <- c(tmp.i, i)
# tmp.org <- paste(tmp.org, tmp[i], sep = "")
}
i <- i + 1
if(i > length(tmp)){
# ret$org.code[[nseq]] <- unlist(strsplit(tmp.org, sep))
ret$org.code[[nseq]] <- unlist(strsplit(tmp[tmp.i], sep))
break
}
}
### check if the inputs are aligned sequences.
flag.aligned <- aligned
tl.seq <- do.call("c", lapply(ret$org.code, length))
if(nseq > 1){
if(any(tl.seq != tl.seq[1])){
flag.aligned <- FALSE
ret$aligned <- FALSE
}
tl.seq <- max(tl.seq)
}
### prepare for return.
ret$nseq <- nseq
ret$seqlen <- tl.seq
ret$seqname <- seqname
if(flag.aligned){
if(byrow){
ret$org.code <- do.call("rbind", ret$org.code)
} else{
ret$org.code <- do.call("cbind", ret$org.code)
}
}
ret$org <- ret$org.code
class(ret) <- "seq.data"
ret
} # End of read.fasta.format().
write.fasta.format <- function(seqdata, filename, classid = NULL,
seqname = NULL, width.line = 60, sep = ""){
if(is.vector(seqdata) && (! is.list(seqdata))){
seqdata <- matrix(seqdata, nrow = 1)
}
### matrix for aligned, list for unaligned.
if(is.matrix(seqdata)){
n.seq <- nrow(seqdata)
} else if(is.list(seqdata)){
n.seq <- length(seqdata)
} else{
stop("The seqdata should be a vector, matirx or list.")
}
if(is.null(seqname)){
seqname <- as.character(1:n.seq)
}
if(!is.null(classid)){
seqname <- cbind(seqname, rep("-", n.seq) , classid)
seqname <- apply(seqname, 1, paste, collapse = "")
}
if(is.matrix(seqdata)){
tl.seq <- ncol(seqdata)
tl.show <- ceiling(tl.seq / width.line)
show.range <- list()
for(i in 1:tl.show){
show.range[[i]] <- (1:width.line) + (i - 1) * width.line
if(show.range[[i]][width.line] > tl.seq){
show.range[[i]] <- show.range[[i]][1:which(show.range[[i]] == tl.seq)]
}
}
ret <- NULL
for(i in 1:n.seq){
ret <- c(ret, paste(">", seqname[i], sep = ""))
for(j in 1:tl.show){
ret <- c(ret, paste(seqdata[i, show.range[[j]]], collapse = sep))
}
}
} else{
ret <- NULL
for(i in 1:n.seq){
tl.seq <- length(seqdata[[i]])
tl.show <- ceiling(tl.seq / width.line)
show.range <- list()
for(j in 1:tl.show){
show.range[[j]] <- (1:width.line) + (j - 1) * width.line
if(show.range[[j]][width.line] > tl.seq){
show.range[[j]] <- show.range[[j]][1:which(show.range[[j]] == tl.seq)]
}
}
ret <- c(ret, paste(">", seqname[i], sep = ""))
for(j in 1:tl.show){
ret <- c(ret, paste(seqdata[[i]][show.range[[j]]], collapse = sep))
}
}
}
write.table(ret, file = filename, quote = FALSE, sep = "",
row.names = FALSE, col.names = FALSE)
} # End of write.fasta.format().
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