R/write.R

In GuangchuangYu/skleid: State Key Lab of Emerging Infectious Diseases

##' write consensus sequence to fasta file
##'
##' 
##' @title writeConsensus
##' @param aln alignment
##' @param output output fasta file 
##' @return NULL
##' @author ygc
##' @importFrom Biostrings DNAStringSet
##' @importFrom Biostrings writeXStringSet
##' @export
writeConsensus <- function(aln, output) {
    ## aln$seqs <- aln$seqs[-1,]
    aln <- aln[-1]
    seq.df <- aln2seqDF(aln)
    idx <- apply(seq.df, 2, function(i) all(i=="-"))
    seq.df <- seq.df[,!idx, drop=FALSE]

    cs <- getConsensus(seq.df)
    cs2 <- DNAStringSet(paste(cs, collapse=""))
    names(cs2) <- sub(".fa[sta]*", "", sub("\\w+/", "", output))
    writeXStringSet(cs2, output)
}