open(MYFILE, $data_file) || die("Could not open file!"); { my $energy; while ( ) { if ( /\bENERGY\b/ ) { ++$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(MYFILE);