Very decent answers above. So this is merely a quibble.

You say

"I do not want to use BioPerl."

Why? ... and why should we not treat such an observation as being of the same order as
"I do not want to use a module." or even,
"I want to dig a hole but I do not want to use a shovel." ?

Using a shovel is usually easier than digging with your bare hands. Using a module is usually easier than reinventing something with its capabilities ... and using BioPerl (seems to be) a well-tested and effective method of achieving your goal.