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

In seqinr: Biological Sequences Retrieval and Analysis

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:
fname <- tempfile(pattern = "ortho3", tmpdir = tempdir(), fileext = "fasta")
#write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = "ortho3.fasta")
write.fasta(sequences = ortho3, names = names(ortho3), nbchar = 80, file.out = fname)

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

seqinr documentation built on May 29, 2024, 6:36 a.m.