my @ids =; my $dir = $opts{d}; chdir($dir) or die "$!"; opendir(DIR, ".") or die "Can't open $dir: $!"; my @files = grep {/fa$/} readdir DIR; close DIR; foreach my $id (@ids) { foreach my $fasta (@files){ local @ARGV = @files; print grep (/$id/,<>), "\n"; } }