foreach my $dir(@subdirs){
    opendir my $dh, "$topdir/$dir" or die "Error: $!";
    my @files = readdir $dh;
    print "raw files = @files\n";
    @files = grep /^(\d+)(.+)(LacZ|pgK|SD|SU)$/,@files;

    print "$dir -> @files\n";
    foreach my $file(@files){
        system( "mv $topdir/$dir/$file $newdir/$file");
    }
    closedir $dh;
}
[download]

When you readdir a directory, you will get a list of files AND subdirs. You need to test the list, and see if any of the results match -d or -f for dir or file. If it matches -d, then run the sub again on it.....it's called recursion.

#!/usr/bin/perl

sub get_sub_dirs {
my $dir = shift;
opendir my $dh, $dir or die "Error: $!";
my @files = grep !/^\.\.?$/, readdir $dh;
closedir $dh;

 for my $file ( @files ) {
    print "$dir/$file\n";
    get_sub_dirs( "$dir/$file" ) if -d "$dir/$file";  
    #notice the -d test, saying it found deeper subdirs
  }
}


$topdir= shift || '.';
get_sub_dirs($topdir);
exit;
[download]

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