-## read.dna.R (2008-03-28)
+## read.dna.R (2012-05-03)
## Read DNA Sequences in a File
-## Copyright 2003-2008 Emmanuel Paradis
+## Copyright 2003-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
read.dna <- function(file, format = "interleaved", skip = 0,
- nlines = 0, comment.char = "#", seq.names = NULL,
- as.character = FALSE)
+ nlines = 0, comment.char = "#",
+ as.character = FALSE, as.matrix = NULL)
{
+ findFirstNucleotide <- function(x) {
+ ## actually find the 1st non-blank character
+ ## just in case: pat.base <- "[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]{10}"
+ tmp <- regexpr("[[:blank:]]+", x[1]) # consider only a single string
+ tmp[1] + attr(tmp, "match.length")
+ }
getTaxaNames <- function(x) {
- x <- sub("^ +", "", x) # remove the leading spaces
- x <- sub(" +$", "", x) # remove the trailing spaces
- x <- sub("^['\"]", "", x) # remove the leading quotes
- x <- sub("['\"]$", "", x) # remove the trailing quotes
+ x <- sub("^['\" ]+", "", x) # remove the leading quotes and spaces
+ x <- sub("['\" ]+$", "", x) # " " trailing " " "
x
}
- format <- match.arg(format, c("interleaved", "sequential", "fasta"))
- phylip <- if (format %in% c("interleaved", "sequential")) TRUE else FALSE
- X <- scan(file = file, what = character(), sep = "\n", quiet = TRUE,
+ getNucleotide <- function(x) {
+ x <- gsub(" ", "", x)
+ x <- strsplit(x, NULL)
+ tolower(unlist(x))
+ }
+ formats <- c("interleaved", "sequential", "fasta", "clustal")
+ format <- match.arg(format, formats)
+ phylip <- if (format %in% formats[1:2]) TRUE else FALSE
+ X <- scan(file = file, what = "", sep = "\n", quiet = TRUE,
skip = skip, nlines = nlines, comment.char = comment.char)
+
if (phylip) {
- fl <- X[1]
- oop <- options(warn = -1)
- ## need to remove the possible leading spaces in the first line
- fl.num <- as.numeric(unlist(strsplit(gsub("^ +", "", fl), " +")))
- options(oop)
- if (all(is.na(fl.num)))
- stop("the first line of the file must contain the dimensions of the data")
- if (length(fl.num) != 2)
- stop("the first line of the file must contain TWO numbers")
- else {
- n <- fl.num[1]
- s <- fl.num[2]
- }
+ ## need to remove the possible leading spaces and/or tabs in the first line
+ fl <- gsub("^[[:blank:]]+", "", X[1])
+ fl <- as.numeric(unlist(strsplit(fl, "[[:blank:]]+")))
+ if (length(fl) != 2 || any(is.na(fl)))
+ stop("the first line of the file must contain the dimensions of the data")
+ n <- fl[1]
+ s <- fl[2]
+ obj <- matrix("", n, s)
X <- X[-1]
- obj <- vector("character", n*s)
- dim(obj) <- c(n, s)
}
- if (format == "interleaved") {
- fl <- X[1]
- fl <- unlist(strsplit(fl, NULL))
- bases <- grep("[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]", fl)
- z <- diff(bases)
- for (i in 1:length(z)) if (all(z[i:(i + 8)] == 1)) break
- start.seq <- bases[i]
- if (is.null(seq.names))
- seq.names <- getTaxaNames(substr(X[1:n], 1, start.seq - 1))
- X[1:n] <- substr(X[1:n], start.seq, nchar(X[1:n]))
- X <- gsub(" ", "", X)
+ switch(format,
+ "interleaved" = {
+ start.seq <- findFirstNucleotide(X[1])
+ one2n <- 1:n
+ taxa <- getTaxaNames(substr(X[one2n], 1, start.seq - 1))
+ X[one2n] <- substr(X[one2n], start.seq, nchar(X[one2n]))
nl <- length(X)
- for (i in 1:n)
- obj[i, ] <- unlist(strsplit(X[seq(i, nl, n)], NULL))
- }
- if (format == "sequential") {
- fl <- X[1]
+ for (i in one2n)
+ obj[i, ] <- getNucleotide(X[seq(i, nl, n)])
+ },
+ "sequential" = {
taxa <- character(n)
- j <- 1
+ j <- 1L # line number
for (i in 1:n) {
- bases <- grep("[-AaCcGgTtUuMmRrWwSsYyKkVvHhDdBbNn?]",
- unlist(strsplit(X[j], NULL)))
- z <- diff(bases)
- for (k in 1:length(z)) if (all(z[k:(k + 8)] == 1)) break
- start.seq <- bases[k]
- taxa[i] <- substr(X[j], 1, start.seq - 1)
- sequ <- substr(X[j], start.seq, nchar(X[j]))
- sequ <- gsub(" ", "", sequ)
- j <- j + 1
- while (nchar(sequ) < s) {
- sequ <- paste(sequ, gsub(" " , "", X[j]), sep = "")
- j <- j + 1
+ start.seq <- findFirstNucleotide(X[j])
+ taxa[i] <- getTaxaNames(substr(X[j], 1, start.seq - 1))
+ sequ <- getNucleotide(substr(X[j], start.seq, nchar(X[j])))
+ j <- j + 1L
+ while (length(sequ) < s) {
+ sequ <- c(sequ, getNucleotide(X[j]))
+ j <- j + 1L
}
- obj[i, ] <- unlist(strsplit(sequ, NULL))
+ obj[i, ] <- sequ
}
- if (is.null(seq.names)) seq.names <- getTaxaNames(taxa)
- }
- if (format == "fasta") {
+ taxa <- getTaxaNames(taxa)
+ },
+ "fasta" = {
start <- grep("^ {0,}>", X)
taxa <- X[start]
+ taxa <- sub("^ {0,}>", "", taxa) # remove the hook and the spaces before
+ taxa <- getTaxaNames(taxa)
n <- length(taxa)
obj <- vector("list", n)
- if (is.null(seq.names)) {
- taxa <- sub("^ {0,}>", "", taxa) # remove the hook and the spaces before
- seq.names <- getTaxaNames(taxa)
- }
start <- c(start, length(X) + 1) # this avoids the following to crash when `i = n'
for (i in 1:n)
- obj[[i]] <- unlist(strsplit(gsub(" ", "",
- X[(start[i] + 1):(start[i + 1] - 1)]),
- NULL))
- }
- if (phylip) {
- rownames(obj) <- seq.names
- obj <- tolower(obj)
+ obj[[i]] <- getNucleotide(X[(start[i] + 1):(start[i + 1] - 1)])
+ },
+ "clustal" = {
+ X <- X[-1] # drop the line with "Clustal bla bla..."
+ ## find where the 1st sequence starts
+ start.seq <- findFirstNucleotide(X[1])
+ ## find the lines with *********....
+ nspaces <- paste("^ {", start.seq - 1, "}", sep = "", collapse = "")
+ stars <- grep(nspaces, X)
+ ## we now know how many sequences in the file:
+ n <- stars[1] - 1
+ taxa <- getTaxaNames(substr(X[1:n], 1, start.seq - 1))
+ ## need to remove the sequence names before getting the sequences:
+ X <- substr(X, start.seq, nchar(X))
+ nl <- length(X)
+ ## find the length of the 1st sequence:
+ tmp <- getNucleotide(X[seq(1, nl, n + 1)])
+ s <- length(tmp)
+ obj <- matrix("", n, s)
+ obj[1, ] <- tmp
+ for (i in 2:n)
+ obj[i, ] <- getNucleotide(X[seq(i, nl, n + 1)])
+ })
+
+ if (format != "fasta") {
+ rownames(obj) <- taxa
} else {
- names(obj) <- seq.names
- obj <- lapply(obj, tolower)
+ names(obj) <- taxa
+ LENGTHS <- unique(unlist(lapply(obj, length)))
+ allSameLength <- length(LENGTHS) == 1
+ if (is.logical(as.matrix)) {
+ if (as.matrix && !allSameLength)
+ stop("sequences in FASTA file not of the same length")
+ } else {
+ as.matrix <- allSameLength
+ }
+ if (as.matrix) {
+ obj <- matrix(unlist(obj), ncol = LENGTHS, byrow = TRUE)
+ rownames(obj) <- taxa
+ }
}
if (!as.character) obj <- as.DNAbin(obj)
obj