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

Description Usage Arguments Value Author(s) References See Also Examples

Description

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

Usage

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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. Nec┼čulea

References

citation("seqinr")

See Also

read.fasta

Examples

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## 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))


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