fetchHmmCombo

#!/usr/bin/env ruby

require 'MySQL'
require 'optparse'

ARGV.options {|opts|
  opts.banner << " hmm-res-file evalue"
  begin
    opts.parse!
  rescue
    STDERR.puts $!.message
    STDERR.puts opts
    exit(1)
  end
  if (ARGV.size < 2)
    STDERR.puts opts
    exit(1)
  end
}

file, evalue = ARGV
evalue = evalue.to_f

db = MySQL.new


ids = []
start = false
File.new(file).each {|line|
  if (start)
    fields = line.chomp.split(" ")
    ids.push(fields[0]) if (fields[9].to_f <= evalue && !fields[0].nil?)
  end
  start = true if (line =~/\[\]/)
  start = false if (line =~/^\n/)
}


ids.each {|id|
  print db.fetchProtID(id)
}