You should really take a look at Bioperl. It ships with a Genbank parser. Would be something like 
my $seq_io = Bio::SeqIO->new( -file => $file, format => 'genbank');
my $whole_genome = $seq_io->next_seq;

[download]
See perldoc Bio::SeqIO.

This parser is quite robust...Which is important as you will notice when you screen many different species ;)

In reply to Re: Genome UV Mutation Script -- Critique by lima1
in thread Genome UV Mutation Script -- Critique by c4onastick

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