#!/usr/local/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 \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;
}
}