Prodigal GFF output and hmmsearch domtblout Merger to GFF

prodigal_pfam_merger.rb

#!/usr/bin/env ruby

require 'pp'

prodigal_file = ARGV[0]
hmmsearch_file = ARGV[1]
hash_id = {}

File.open(hmmsearch_file) do |ios|
  ios.each_line do |line|
    line.chomp!
    fields = line.split "\t"
    hash_id[fields[0]] = [fields[1],fields[2]]
    end
  end
File.open(prodigal_file) do |ios|
  ios.each_line do |line|
    if line[0] != '#'
      fields = line.split "\t"
      attributes = fields.last.split ";"
      hash_id.each do |key, val|
        if fields[0] == key
          attributes[2] = val[0]
          attributes[3] = val[1]
        end
      end
      fields[-1] = attributes.join ";"
      line = fields.join "\t"
      puts line
    end
  end
end