I am getting a headache trying to read your post. Please edit your post and change your <end code> to </CODE>.

I fear you do not understand how chdir works in Perl. After calling chdir, you must call getcwd() again to refresh your $current_dir variable. Please run this program and let us know what it prints:

# change_directory.pl

use warnings;
use strict;
use Cwd;

my $current_dir = getcwd();

#list the Timepoint directories
my @TP_dir = glob("T*");

for my $dir (@TP_dir) {
   my $fulldir = "$current_dir/$dir";
   if (-d $fulldir) {
      chdir($fulldir) or die "error: chdir '$fulldir': $!";
      my $currdir = getcwd();
      print "cd worked: currdir is now '$currdir'\n";
   }
   else {
      print "oops: '$fulldir' is not a dir\n";
   }
}
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In perlfaq8, look at the question "I {changed directory, modified my environment} in a perl script. How come the change disappeared when I exited the script? How do I get my changes to be visible?"

glob("T*") will return all the files (and directories) in your current directory which contain an upper or lower case "T". There's no assurance that the directories will appear at the head of the list (it's sorted ascii-beticly). In other words, $TP_dir[0] may very well contain a file. Cconsider, for example, a directory like this:

dir
      T1
      T2
      _t.txt
      foo.txt
      bar.txt
      ~out.out
      out.c
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See eyepopslikeamosquito's response for the method of testing if you must use glob.

And, as others have said, please read-and-heed-and-use the Monastery's modified html markup standards and/or Markup in the Monastery so we need not go to such trouble to read your post.

Using readdir and grep{} will work on any version of Perl and on any platform. Important to know is that readdir only returns the file names in the directory - not the full path name. So when you do the tests in grep{} to filter out non-directories, you have to use the full path on the -d test. Since you can use a regex inside the grep{}, you can get exactly what you want even if it is much more complex than the example below.

In general, I would advise against using cwd to change your working directory. Use full pathnames or relative pathnames from where your program is running. That way, you won't get confused about "where you are", ie where your program is running.And later in the program if you need to do something like delete some file (or perhaps make a sub-directory), you know exactly how to get a valid path name which will allow that. Plus see how much "cleaner" the code looks.

I use the following "formula"...

#!/usr/bin/perl 

use warnings; 
use strict; 

#list the Timepoint directories 

my $dir = ".";
opendir (DIR, $dir) || die "couldn't open directory $dir\n";

my @TP_dirs = grep{-d "$dir/$_" && /^T/ }readdir DIR;

foreach (@TP_dirs)
{
   print "relative path of TP:  $dir/$_\n";
}

__END__
in my dir, prints: relative path of TP:  ./TESTING
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