#!/usr/bin/perl
# Author: Haoyuan Zhu
# Description: Change metameme output to web version
# We need to change the name of HMM file, Sequence file, Motif file

#SDSC setting:
$weboutputdir = "http://metameme.sdsc.edu";

if ($#ARGV < 2){
    print stderr "USAGE: changetoweb.pl <input file> <Sequence file name> <Motif file name>\n";
    exit(0);
}

$infile = $ARGV[0];
$motif_name = $ARGV[1];
$seq_name = $ARGV[2];
open ($infile,"<$infile") || die "Cannot open $infile\n";
$mark = 0; # Have we reached parameters part?
while ($line = <$infile>){
    if ($line =~ /Program parameters/){
	$mark = 1;
    }
    if ($mark != 1){
	if (($line =~ /HMM file/) || ($line =~ /Database file/)){
	    @temp1 = split(':',$line);
	    @temp2 = split('website',$temp1[1]);
	    chomp($temp3 = $temp2[1]);
	    if ($line =~ /HMM file/){
	    	print "$temp1[0]: $weboutputdir$temp3\n";
	    }
	    elsif ($temp3 eq ""){
		print "$temp1[0]: $seq_name\n";
	    }
	    else{
		print $line;
	    }
	}
	elsif (($line =~ /Sequence file/) || ($line =~ /sequence_file/)){
	    @temp = split(':',$line);
	    print "$temp[0]: $seq_name\n";
	}
	elsif (($line =~ /Motif file/) || ($line =~ /motif_file/)){
	    @temp = split(':',$line);
	    print "$temp[0]: $motif_name\n";
	}
	else{
	    print $line;
	}
    }
    else{
	print $line;
    }
}