Untested

use Bio::SeqIO;

$infile  = Bio::SeqIO->new(-file => $ARGV[0] , '-format' => 'Fastq');
$outfile = Bio::SeqIO->new(-file => ">myfilename" , '-format' => 'genb
+ank');

while ( my $seq = $infile->next_seq() ) {

     ...do something... 

# finally you could print to $outfile in genbank format 
(for example... or in embl, nexml, bsml, fasta, seqxml...)

     $outfile->write_seq($seq); 
     }
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