concepts2.pl 
 
#!/usr/bin/perl 
use strict; 
use CGI; 
my $cgi=new CGI; 
 
 
print $cgi->header(); 
print $cgi->start_html(-title=>'Form Results', 
                       -author=>'BoChak'); 
 
#my $file=$cgi->param('file'); 
my $file="/root/Desktop/test.fasta"; 
 
print "<br> $file <br>"; 
 
################ Process File ######################### 
#my $file=<>; 
my $seqname=''; 
my $sequence=''; 
my %seqhash=(); 
 
open (FILE,"<$file") or die "Can't open $file\n"; 
 
while (my $line=<FILE>){ 
  chomp($line); 
 
  if ($line=~m/^>/){ 
     my @temp=split(' ',$line);  
     $seqname=substr($temp[0],1); 
  } 
  
  elsif ($line=~m/^\s$/||$line=~m/^$/){ 
     $seqhash{$seqname}=$sequence; 
   
  } 
 
  else { 
     $sequence=$sequence.$line; 
    
  } 
} 
close (FILE); 
######################################################## 
 
 
 
foreach my $key (keys %seqhash){ 
    my $risk=docParser->new($key, $seqhash{$key} ); 
    $risk->CAG_count(); 
} 
 
 
print $cgi->end_html."\n";