seqinr (version 1.0-1)

write.fasta: Write file in fasta format

Description

Writes sequences to a file in FASTA format.

Usage

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

Arguments

sequences

A DNA or protein sequence (i.e. a character vector) or a list of sequences (i.e. a list of character vectors).

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

• NULL

References

citation("seqinr")

See Also

read.fasta

Examples

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

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

Run the code above in your browser using DataCamp Workspace