$ # String longer than 6 characters
$ perl -e '$a="1234567"; $b=sprintf("%6s", substr($a, 0, 6)); print $b;'
123456
$ # String shorter than 6 characters
$ perl -e '$a="123"; $b=sprintf("%6s", substr($a, 0, 6)); print $b;'
   123
$ # Example of results from OP's code
$ perl -e '$a="1234567"; $b=substr($a, 0, 6); print $b;'
123456
$ perl -e '$a="123"; $b=sprintf("%6s", substr($a, 0)); print $b;'
   123