Nothing
#
# Read files of aligned sequences in various formats
#
read.alignment <- function(file, format, forceToLower = TRUE, ...)
{
#
# Check if the file is an URL:
#
urlcheck = substr(file, 0,4)
if (urlcheck == "http") {
# Copy the contents to a tmpfile to be read later
lines <- readLines(file)
tmpaln <- tempfile(pattern = "readaln")
writeLines(lines,tmpaln)
file <-tmpaln
}
#
# Check that we have read permission on the file:
#
file <- path.expand(file)
if(file.access(file, mode = 4) != 0) stop(paste("File", file, "is not readable"))
fasta2ali <- function(file, ...){
tmp <- read.fasta(file, as.string = TRUE, ...)
list(length(tmp), getName(tmp), unlist(getSequence(tmp, as.string = TRUE)))
}
ali <- switch( tolower(format),
fasta = fasta2ali(file, ...),
mase = .Call("read_mase", file, PACKAGE = "seqinr"),
phylip = .Call("read_phylip_align", file, PACKAGE = "seqinr"),
msf = .Call("read_msf_align", file, PACKAGE = "seqinr"),
clustal = .Call("read_clustal_align", file, PACKAGE = "seqinr"),
stop("Wrong format name: Format available are fasta, mase, phylip, msf, clustal")
)
ali <- lapply(ali, as.character)
#cleaning \r char
ali <- lapply(ali, function (x ){gsub ('\r','',x)})
if(forceToLower) ali[[3]] <- lapply(ali[[3]], tolower)
if(format == "mase"){
ali <- list(nb = as.numeric(ali[[1]]), nam = ali[[2]], seq = ali[[3]], com = ali[[4]])
} else {
ali <- list(nb = as.numeric(ali[[1]]), nam = ali[[2]], seq = ali[[3]], com = NA)
}
class(ali) <- "alignment"
return(ali)
}
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