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#!/usr/bin/perl
use strict;
use warnings;
...
while ( my $seq = $in->next_seq() ) {
    $out->write_seq($seq);
}

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>NC_004905 Influenza A virus (A/Hong Kong/1073/99(H9N2)), complete gen
+ome.
AGCAGGGTTAATAATCACTCACTGAGTGACATCAACATCATGGCGTCGCAAGGCACCAAA
CGATCCTATGAACAGATGGAAACTGGTGGAGAACGCCAGAATGCCACTGAGATCAGGGCA
...
ATGGAAAGTGCCAGACCAGAAGATGTGTCTTTCCAGGGGCGGGGAGTCTTCGAGCTCTCG
GACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGATCTTAT
TTCTTCGGAGACAATGCAGAGGAATATGACAATTGAGGAAAAATACCCTTGTTTCTA