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>header1
AGACATGATCGACTGGACACAATTTACGTAGCTG
>header2
AAATACTAGGGCAACACACACACACACCACACAC
>header3
AGTTAGTCCAGTAGTTTACAGTACGACTGATCGT

my $fasta = $ARGV[0];
my $seqio = Bio::SeqIO->new(-file => $fasta);
while(my $seqobj = $seqio->next_seq) {
...
while (<$IN2>) {
    # Subsample the FASTA sequences
}