Rename fasta identifiers

README.md

Rename Fasta IDs

This script is needed for programs like secretomep that truncate fasta ids.
We need to be able to uniquely identify each fasta entry so this script renames the ids with a numeric scheme It also produces a mapping file from old to new ids so the original ids can be recovered later

Use it like this

  ./rename_fasta.rb yourfasta.fasta

If you get an error about permissions you may need to do this first

  chmod u+x rename_fasta.rb

rename_fasta.rb

#!/usr/bin/env ruby

# ARGV holds command line arguments.  In this case it will be the name of our input fasta
fastafile=ARGV.shift

# Open two files for output. 
new_fasta = File.open("#{fastafile}_rename.fasta","w+") #One for the new fasta file
new_old_mapping = File.open("#{fastafile}_mapping.txt","w+") # One for the mapping

# A counter for creating the numeric new ids
seqnum = 0

# Loop over the original fasta file
File.foreach(fastafile) do |line|  
        
        # Use a regex to match fasta description lines
        id_match = line.match(/^>([^ ]*)/)

        # If it is a description line then do extra stuff
        if id_match
                seqnum += 1
                
                # Extract the original id
                old_id = id_match.captures[0]
                new_id = "S#{seqnum}"
                
                # Create a new line with the new id 
                line.sub!(old_id,new_id)
                
                new_old_mapping.write "#{old_id}\t#{new_id}\n"

        end
        
        new_fasta.write line
end