print "@ids\n";
print "@files\n";
##</code><code>##

foreach my $id (@ids) {
    foreach my $fasta (@files) {
        open my $fh, '<', $fasta or die "can not open file $fasta: $!";
        while (<$fh>) {
            print if /$id/;
        }
        close $fh;
    }
}
##</code><code>##

my $pattern = join '|', @ids;
print grep {/$pattern/} <>;