Nothing
"write.fasta" <-
function(alignment=NULL,
ids=NULL,
seqs=alignment$ali,
gap=TRUE,
file,
append = FALSE) {
if (is.null(seqs))
stop("write.fasta: please provide a 'seqs' or 'alignment' input object")
if (!is.null(alignment)) {
if (is.null(alignment$id) | is.null(alignment$ali)) {
stop("write.fasta: 'alignment' should be a list with '$id' and '$ali'components")
}
if (is.null(ids)) {
ids=alignment$id
}
} else {
if (is.null(ids)) {
n.ids <- nrow(seqs)
if(is.null(n.ids)) { n.ids=1 }
ids=seq( 1, length=n.ids )
}
}
if(!gap) {
seqs[is.gap(seqs)] <- ""
}
if (!append) {
##file.remove(file, showWarnings = FALSE)
suppressWarnings( file.remove(file) )
}
nseqs <- length(ids)
if (nseqs == 1) {
# change for shortening lines (<=60) - Xinqiu
cat(">", ids, "\n", file = file, append = TRUE, sep = "")
cat(seqs, file = file, append = TRUE, sep = "", fill = 60)
# cat(">", ids, "\n", seqs, "\n", file = file,
# append = TRUE, sep = "")
}
else {
for (i in 1:nseqs) {
cat(">", ids[i], "\n", file = file, append = TRUE, sep = "")
cat(seqs[i,], file = file, append = TRUE, sep = "", fill = 60)
# cat(">", ids[i], "\n", seqs[i,],
# "\n", file = file, append = TRUE, sep = "")
}
}
}
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