Write sequence(s) into a file in fasta format
Writes one or more sequences into a file in FASTA format.
write.fasta(sequences, names, file.out, open = "w", nbchar = 60, as.string = FALSE)
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. |
none.
A. Necşulea
citation("seqinr")
## 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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.