aliasFasta

#!/usr/bin/env ruby
 
require 'rubygems'
require 'bio'

if (ARGV.size != 3)
 STDERR.printf("usage: %s fasta out-fasta alias-file\n", $0)
 exit(1)
end

fasta, out, ali = ARGV

outFile = File.new(out, "w")
aliFile = File.new(ali, "w")


orfNum = "SID000001"
Bio::FlatFile.new(Bio::FastaFormat, File.new(fasta)).each do |seq|
 aliFile.printf("%s\t%s\n", orfNum, seq.definition)
 seq.definition = orfNum
 outFile.print seq
 orfNum = orfNum.succ
end

outFile.close
aliFile.close