#!/usr/bin/perl
# File: oldmeme2meme
# Author: Haoyuan Zhu
# create Date: 12/7/01
# Project: MHMM
# Description: Given a old MEME file, return 
#              a new MEME file's content

if (scalar(@ARGV) != 1) {
  print ("USAGE: oldmeme2meme <old MEME file>\n");
  exit(1);
}
($old_meme_file) = @ARGV;

$motif_summary_begin = "<INPUT TYPE = HIDDEN NAME = motif-summary VALUE = \"";
$motif_summary_end = ">";

$new_meme = "";
$num_seq = 0;
$seq_occur = 0;
open(IN,"<$old_meme_file") || die("Cannot open $old_meme_file\n");
while ($line = <IN>){
  if ($line =~ /Sequence name/){
    $new_meme .= $line;
    $line = <IN>;
    $new_meme .= $line;
    $line = <IN>;
    while (!($line =~ /PRE/) and !eof){
      #$line = <IN>;
      $new_meme .= $line;
      @temp = split(' ',$line);

      #
      # Below is very silly code to deal with different MEME version - Haoyuan Zhu (3/30/02)
      #
      if ($temp == 5){
	$name_seq[$num_seq] = $temp[0];
	$length_seq[$num_seq] = $temp[2];
	$num_seq ++;
	$name_seq[$num_seq] = $temp[3];
	$length_seq[$num_seq] = $temp[5];
	$num_seq ++;
      }
      elsif ($#temp == 2){
	$name_seq[$num_seq] = $temp[0];
	$length_seq[$num_seq] = $temp[2];
	$num_seq ++;
      }
      elsif ($#temp == 1){
	$name_seq[$num_seq] = substr($temp[0],0,23);
	$length_seq[$num_seq] = $temp[1];
	$num_seq ++;
      }
      elsif ($#temp == 3){
	$name_seq[$num_seq] = substr($temp[0],0,23);
	$length_seq[$num_seq] = $temp[1];
	$num_seq ++;
	$name_seq[$num_seq] = substr($temp[2],0,23);
	$length_seq[$num_seq] = $temp[3];
	$num_seq ++;
      }
      elsif ($#temp == 4){
	if (length($temp[0]) > 24){
	  $length_seq[$num_seq] = $temp[1];
	  $num_seq ++;
	  $length_seq[$num_seq] = $temp[4];
	  $num_seq ++;
	}
	else{
	  $length_seq[$num_seq] = $temp[2];
	  $num_seq++;
	  $length_seq[$num_seq] = $temp[4];
	  $num_seq++;
	}
      }
      # End of silly code
      
      $line = <IN>;
#      print STDERR "here\n";
    }
    
    $new_meme .= $line;
  }
  
  elsif ($line =~ /$motif_summary_begin/){
    $new_meme .= $line;
    $line = <IN>;
    while (!($line =~ /$motif_summary_end/)){
      #$line = <IN>;
      $new_line = "";
      $seq_occur ++;
      @temp = split(' ',$line);
      if ($#temp % 3 != 0){
	for ($i=0;$i<3;$i++){
	  $new_line = $new_line.$temp[$i]." ";
	}
	$new_line = $new_line.$length_seq[$seq_occur-1]." ";
	for ($i=3;$i<$#temp;$i++){
	  $new_line = $new_line.$temp[$i]." ";
	}
	$new_line = $new_line.$temp[$i]."\n";
	$new_meme  = $new_meme.$new_line;
	$line = <IN>;
      }
      else{
	$new_meme .= $line;
	$line = <IN>;
      }
    }
    $new_meme .= $line;
    
    
  }
  else{
    $new_meme .= $line;
  }
}
#print stderr $#length_seq;
print "$new_meme";