my $gb=new Bio::DB::GenBank;

open my $handle, '<', 'sec.txt' or die !$; # check for success

while ( my $line = <$handle> ) {           # read one line at a time
    chomp $line;                           # strip new line chars
    print "Doing $line\n";

    my $seq = $gb->get_Seq_by_id( $line );
    write_sequence (">>roar.fa", 'fasta',$seq );
                   # ^^
                   # ( assuming write_sequence() supports appending )
}

close $handle or die $!;