$data_file="HIVgag.ct";

open(MYFILE, $data_file) || die("Could not open file!");
$b=$between=$energy=0;
while (<MYFILE>) {
    if (/energy/i) {
        $energy++;
        $between=$b;
    }
    elsif ($energy) {$b++}
}

print "$energy / $between\n";
close(MYFILE);

open(MYFILE, $data_file) || die("Could not open file!");
open(WRITE, ">final.net");
print WRITE "*vertices $between\n";

 while(<MYFILE>)
 {
 foreach $row (<MYFILE>)
 {
 @row = $row;
(@row[0],@row[1],@row[2], @row[3], @row[4], @row[5], @row[6])=split(/\s+/,$row);
if (@row[2] ne ENERGY)
{
 print  WRITE "@row[1]  $row[2]\n";
 print"@row[1]  $row[2]\n";
 }
    }
 }
 close(MYFILE);
 
 open(MYFILE, $data_file) || die("Could not open file!");
 {
print WRITE "*edges\n";
my $energy;
while ( <MYFILE> ) {
    if ( /\bENERGY\b/ ) {
        ++$energy;
        next;
       }
	   
    my ( $key, @fields ) = grep $_, split;
    for my $field ( @fields ) {
	if ( $field ne 'G' && $field ne 'A' && $field ne 'C' && $field ne 'G' )
	{
        print WRITE "$key $field $energy\n";
        }
    }
	}
	}
close(WRITE);