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#
# Read files of aligned sequences in various formats
#
read.alignment <- function(file, format, forceToLower = TRUE)
{
#
# 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"))
ali <- switch( format,
fasta = .Call("read_fasta_align", file, PACKAGE = "seqinr"),
FASTA = .Call("read_fasta_align", file, PACKAGE = "seqinr"),
mase = .Call("read_mase", file, PACKAGE = "seqinr"),
MASE = .Call("read_mase", file, PACKAGE = "seqinr"),
phylip = .Call("read_phylip_align", file, PACKAGE = "seqinr"),
PHYLIP = .Call("read_phylip_align", file, PACKAGE = "seqinr"),
msf = .Call("read_msf_align", file, PACKAGE = "seqinr"),
MSF = .Call("read_msf_align", file, PACKAGE = "seqinr"),
CLUSTAL = .Call("read_clustal_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)
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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