Check CPAN for modules that might already do this. A search on CPAN provides quite a few interesting options.

Ex. Boulder::Blast::NCBI

Take a look at perldoc for basics like perldata and Getopt Long

Take a shot at those and when you run into issues, show your work and ask questions.

#!/usr/bin/perl
use strict;
use warnings;
use Boulder::Blast::NCBI; #or whatever might work best for you
...
[download]

Hope that is helpful...