R: Write sequence(s) into a file in fasta format

write.fasta {seqinr} | R Documentation

## Write sequence(s) into a file in fasta format

### Description

Writes one or more sequences into a file in FASTA format.

### Usage

    write.fasta(sequences, names, file.out, open = "w", nbchar = 60, as.string = FALSE)

### Arguments

`sequences` | A DNA or protein sequence (in the form of a vector of single characters by default) or a list of such sequences.
`as.string` | FALSE. When set to TRUE sequences are in the form of strings instead of vectors of single characters.
`names` | The name(s) of the sequences.
`nbchar` | The number of characters per line (default: 60)
`file.out` | The name of the output file.
`open` | Mode to open the output file, use "w" to write into a new file, use "a" to append at the end of an already existing file.

### Value

none.

### Author(s)

A. Necşulea

### References

`citation("seqinr")`

### See Also

`read.fasta`

### Examples

    ## Read 3 sequences from a FASTA file:
    ortho <- read.fasta(file = system.file("sequences/ortho.fasta", package =
    "seqinr"))

    ## Select only third codon positions:
    ortho3 <- lapply(ortho, function(x) x[seq(from = 3, to = length(x), by = 3)])

    ## Write the 3 modified sequences to a file:
    write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = "ortho3.fasta")

    ## Read them again from the same file and check that sequences are preserved:
    ortho3bis <- read.fasta("ortho3.fasta", set.attributes = FALSE)
    stopifnot(identical(ortho3bis, ortho3))

[Package seqinr version 3.4-5 Index]