#!/usr/local/bin/perl
# Prilusky, 2009

  $|=1;
  my $fasta   = "/usr/local/bin/fasta35";
  my $library = "~student/../data/pdb_seqres.txt";
  my $query   = "~student/../data/2ace.fasta";
  my $options = "-Q -H -d 0 -E 5 -F 0.01";

  my $command = "$fasta $options $query $library";
  print "Start running\n$command\n";

  local(*FH);
  open(FH,"$command |");
  while ($l = <FH>) {
    next if ($l =~ /^ *$/);
    if ($l =~ /The best scores are/) { $inData++; next;}
    next if (!$inData);
    last if ($l =~ /^\d+ residues in/);
    print $l;
  }
  close(FH);

  print "Done.\n";