Why do you not, in place of the if statement, just do: $conv = sprintf("%6f" substr($line, 0, 6));. In the case of a string longer than 6 characters, it returns only the leftmost 6 characters; in the case of a string shorter than 6 characters, it returns a string padded on the left with spaces.

Testing:

$ # 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
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Hope that helps.