as.fasta {msaR}

as.fasta

Description

functionality to convert objects to a fasta string. Currently this can handle character objects which are interpreted as filenames or several of the popular means of storing sequence data: DNAbin, DNAStringSet, AAStringSet, RNAStringSet, BStringSet, DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment.

Usage

as.fasta(seqs)

Arguments

seqs

(Required.) the sequence/alignment to be displayed. A character vector, DNAbin, DNAStringSet, AAStringSet, or RNAStringSet.

Value

A character string in fasta format.

Examples

seqfile <- system.file("sequences","AHBA.aln",package="msaR")
as.fasta(seqfile)
help("as.fasta")

## Not run: 
if (requireNamespace("Biostrings")) {
   seqs <- readDNAStringSet(seqfile)
   as.fasta(seqs)
 }

## End(Not run)