my ($self) = @_;

  my $filehandle;
  my $resfile = $self->resultsfile();
  my @fps;
		

  if (-e $resfile) {
    if (-z $resfile) {  
      print STDERR "Prints didn't find any hits\n";
      return; 
    } else {
      open (CPGOUT, "<$resfile") or $self->throw("Error opening ", $resfile, "\n "); # 
    }
  }


  my $id;
  my $line;
  
  my $sequenceId;
  my @features;
  my %evalue;
  my %printsac;

  while (<CPGOUT>) {
    $line = $_;

    print STDERR "Next line: $line";
    chomp $line;
    # Pattern match the Sn; field which should contain the SequenceId and Accession
    
    if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:

      #ENSP00000003603 Gene:ENSG00000000003 Query:AL035608 Contig:AL035608.00001 Chr:chrX basepair:97227305
      ($sequenceId) = $line =~ /^\s*(\w+)/;
    }


    if ($line =~ s/^1TBH//) {
      my  ($id) = $line =~ /^\s*(\w+)/;
      my ($ac) = $line =~ /(PR\w+)[;\.]*\s*$/;
      $printsac{$id} = $ac;
      print STDERR "1TBH line = $line\n";
      print STDERR "In 1TBH data, printsac{$id} =  $ac\n";
    }

# get the evalues of each of the fingerprint names
    if ($line =~ /^2TBH/) {
      print STDERR "got a 2TBH line: $line\n";
      my @line = split /\s+/, $line;
      $evalue{$line[1]} = $line[9];
      print STDERR "hash evalue of $line[1] = $line[9]\n";
    }

    if ($line =~ s/^3TB//) {
      if ($line =~ s/^[HN]//) {
	my ($num,$temp1,$tot1) = "";
	# Grab these lines
	#       1433ZETA        1  of  6  88.19   1328    1.00e-16  ELTVEERNLLSVAYKNVIGARRASWRIITS  30   35   36   48
	# split line on space, hence strip off all leading spaces first.
	$line =~ s/^\s+//;
	print STDERR "line = $line\n";
	# Place all elements of list into an array
	my @elements = split /\s+/, $line;

	# Name each of the elements in the array
	my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements;
	print STDERR "fingerprintName=$fingerprintName\n";
	my $start = $matchPosition;
	#
	# If the match to the pattern lies at the end of the protein we might get padding of the subsequence with #'s, and the
	# end position will be bigger than the actual end of the protein. So we'll strip the #'s off the end, adjust the
	# motif length accordingly, and only then derive the match end.
	my $hash_substring;
	my $end;
	
	if($subsequence =~ /(\#+)$/){
	  $hash_substring = $1;
	  $end = $matchPosition + $motifLength - 1 - length($hash_substring);
	} else {
	  $end = $matchPosition + $motifLength - 1;
	}
	
# if we don't have a valid hit for this PRINTS ID, then ignore teh rest
	if (! exists $printsac{$fingerprintName}) {next;} 

	my $print =  $printsac{$fingerprintName};
	my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$evalue{$fingerprintName}";
	print STDERR "features= $feat\n";
	
	print "matched\n";
	my $hstart = 0;
	my $hend = 0;
	my $evalue = $evalue{$fingerprintName};

	print STDERR "writing to database\n";
	my $fp= $self->create_protein_feature($start, $end, $profileScore, $sequenceId, $hstart, $hend, $print, $self->analysis, $evalue, $percentageIdentity);
	push @fps, $fp;
      }
    }
  }

  close (CPGOUT); 
  $self->output(\@fps);
}

1;

    my ($self) = @_;

    # run program
    print STDERR "running ".$self->program." against ".$self->database."\n";

    print STDERR "FILENAME: ".$self->queryfile."\n";
 
    my $cmd = $self->program .' '.
		$self->database .' '.
                $self->queryfile. ' '.
	        $self->analysis->parameters .' '.
		'> ' . $self->resultsfile;
    print STDERR "$cmd\n";   
    $self->throw ("Error running Prints_wormbase ".$self->program." on ".$self->filename) 
	unless ((system ($cmd)) == 0);

 Title    : run_program
 Usage    : $self->program
 Function : makes the system call to program
 Example  :
 Returns  : 
 Args     :
 Throws   :