Save a proteome in fasta format — write.proteome • orthologr

This function takes a proteome (in data.table notation) as returned by read.proteome and saves it to your hard drive.

write.proteome(proteome, file.name, nbchar = 80, open = "w", as.string = TRUE)

Arguments

proteome: a data.table object storing amino acid sequences in the first column and gene ids in the second column. See read.proteome for details.
file.name: a character string specifying the name of the fasta output file.
nbchar: number of characters per line.
open: mode to open the output file, you can choose from "w" to write into a new file, or "a" to append at the end of an already existing file.
as.string: when set to TRUE sequences are in the form of strings instead of vectors of single characters.

Author

Hajk-Georg Drost

Examples


if (FALSE) {

# read an example proteome
Ath.proteome <- read.proteome(
                      system.file('seqs/ortho_thal_aa.fasta', package = 'orthologr'), 
                      format = "fasta")

# use the write.proteome function to store it on your hard drive
write.proteome(Ath.proteome, "test_proteome.fasta")

}