readdir() attempted on invalid dirhandle $par_dir - perl

Question

I am trying just to execute a perl script inside multiple folders, but I don't understand why I have a problem with readdir() attempted on invalid dirhandle $par_dir. $parent is printed good but $par_dir is printed like "GLOB(0x17e7a68)".
Any idea of why it is happening? Thanks a lot!
Here the code:
#!/usr/bin/perl
use warnings;
use Cwd;
use FileHandle;
use File::Glob;
my $parent = "/media/sequentia/NAS/projects/131-prgdb3/01- DATA/All_plant_genomes_proteomes";
my ($par_dir, $sub_dir);
opendir($par_dir, $parent);
print $parent."\n";
print $par_dir."\n";
while (my $sub_folders = readdir($par_dir)) {
next if ($sub_folders =~ /^..?$/); # skip . and ..
my $path = $parent . '/' . $sub_folders;
next unless (-d $path); # skip anything that isn't a directory
print $path."\n";
chdir($path) or die;
#files = glob( $path. '/*' );
foreach $filename (#files){
print $filename ."\n";
system ("grep 'comment' PutativeGenes.txt | wc -l");
system ("grep 'class' PutativeGenes.txt | wc -l");
}
}
closedir($par_dir);

Answer 1

The problem is probably that the directory you specify in $parent doesn't exist. You must always check to make sure that a call to open or opendir succeeded before going on to use the handle
That path step 01- DATA is suspicious. I would expect 01-DATA or perhaps 01- DATA with a single space, but multiple spaces are rarely used because they are invisible and difficult to count
Here are some other thoughts on your program
You must always use strict and use warnings 'all' at the top of every Perl program you write. That will alert you to many simple errors that you may otherwise overlook
Your statement next if ( $sub_folders =~ /^..?$/ ) is wrong because the dots must be escaped. As it is you are discarding any name that is one or two characters in length
If your path really does contain spaces then you need to use File::Glob ':bsd_glob', as otherwise the spaces will be treated as separators between multipl glob patterns
You execute the foreach loop for every file or directory found in $path, but your system calls aren't affected by the name of that file, so you're making the same call multiple times
It's worth noting that glob will do all the directory searching for you. I would write something like this
#!/usr/bin/perl
use strict;
use warnings 'all';
use File::Glob ':bsd_glob';
my $parent_dir = "/media/sequentia/NAS/projects/131-prgdb3/01-DATA/All_plant_genomes_proteomes";
print "$parent_dir\n";
while ( my $path = glob "$parent_dir/*" ) {
next unless -d $path;
print "$path\n";
chdir $path or die qq{Unable to chdir to "$path": $!};
while ( my $filename = glob "$path/*" ) {
next unless -f $filename;
print "$filename\n";
system "grep 'comment' PutativeGenes.txt | wc -l";
system "grep 'class' PutativeGenes.txt | wc -l";
}
}

Answer 2

Probably opendir() is failing giving the invalid file handle (probably it fails because you try to open a nonexistent $parent directory).
If opendir fails it will return false, and $par_dir is left unchanged as undef. If you attempt to call readdir() on an undefined file handle you will get a runtime warning like:
readdir() attempted on invalid dirhandle at ...
Therefore you should always check the return code from opendir. For example, you can do:
opendir($par_dir, $parent) or die "opendir() failed: $!";
or see more suggestions on what to do in this link Does die have to be used if opening a file fails?
Note that your code could have been simplified using File::Find::Rule, for example:
my #dirs = File::Find::Rule
->directory->maxdepth(1)->mindepth(1)->in( $parent );
for my $dir (#dirs) {
say "$dir";
my #files = File::Find::Rule->file->maxdepth(1)->in( $dir );
say "--> $_" for #files;
}
Alternatively, if you don't need the directory names:
my #files = File::Find::Rule
->file->maxdepth(2)->mindepth(2)->in( $parent );
say for #files;