write.proteome: Save a proteome in fasta format

In HajkD/orthologr: Comparative Genomics with R

Save a proteome in fasta format

Description

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

Usage

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(s)

Hajk-Georg Drost

Examples

## Not run: 

# 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")


## End(Not run)

HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.