compile : perl  prog.pl  input.db  result
#! /usr/local/bin/perl -w

#initialize all the variable, initialize flags to 0 and line to ''

my $counter=1;
my $file1="$ARGV[0]";
my $result=">".$ARGV[1];
my $site='';
my $titleline='';
my $siteflag=0;
my $titleflag=0;

open(INFO1,$file1) or die "Can't open $file1.\n";   #open file1
open(OUT,$result) or die "Can't open $result.\n";   #open result  

#the input files has a separator :\r\n in each line
foreach(<INFO1>)
{                   

  if(/\s*TITLE\s*(.*)\r/){
    ######## check the title
        $titleflag=1;
        $titleline=$1;
    }                              
   elsif(/\s*\/interaction_site=(.*)\r/){
     ######## handle the title
        print OUT qq(References:TITLE\t "$titleline"\n);
        $titleflag=0;
        $titleline=''; 
     ########  check the site   
       $site=$1;
       $siteflag=1;
    }      
    elsif(/\s*(.*)\r/ && $titleflag==1){
        $titleline.=" "; # add a white space
        $titleline.=$1;  #concatenate the title with previous line
    }                      
                                           
    elsif(/\s*\/channel=(.*)\r/){
        if(check2($1)){
        print OUT "Channel\t $1\n";
        }
    }
    elsif(/\s*\/target_cell=(.*)\r/){
        if(check2($1)){
        print OUT "Target_cell\t $1\n";
        }
    }
    elsif(/\s*\/c_end=(.*)\r/){
    ######## handle interaction site
        $siteflag=0;
        $site='';
   
    ######## check c_end
        if(check2($1)){
            print OUT "C_end\t $1\n";
      }# end if
    }#end elsif
    
    ####elsif(/\s*(.*)\r && $siteflag==1){
    ####   $site.=" "; # add a white space
    ####    $site.=$1; #concatenatewith previous site
    ####    print "Site $site\n";
    ####    }    

} # end foreach

sub check2 { #check whether item = empty quotes
    if($1 =~ /" "/){
        return 0;}
    else{
        return 1;}
}