This program needs to be automated to the point of taking a given folder (stated by user), and assigning a filehandle to each text file. Once this is done, I need to be able to reference each so my basic parsing element can act on each file and converge the data into one output file.

If I read that right, you want to have all of the filehandles at the same time, presumably so you can read from each as you need to rather than process the files sequentially. This mostly untested code:

sub get_filehandles {
    my $dir = shift;
    opendir my ($dh), $dir;

    my @fhs = map {
        my $fh;
        open( $fh, '<', "$dir/$_" ) ? $fh 
                                    : do { warn "$dir/$_: $!"; () }
    } grep { -f "$dir/$_" } readdir($dh);

    closedir $dh;
    return \@fhs;
}
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Update: Fixed a bug. I was always returning the filehandle whether it was successfully opened or not. It shouldn't barf with warnings on now. I also tried to improve its readability a bit.

-sauoq
"My two cents aren't worth a dime.";

opendir(DIR, $directory) or die "Failed to open $directory: $!";

while (defined($filename = readdir(DIR))) {
  #Do stuff to each file $filename
}
closedir(DIR);
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I have tried to implement your suggested code into the program, but have found it isn't workig very well. Apparently, it is unable to open the directory. This could be because I'm not entering the name in a readable form, but I'm not sure. Here's where I'm at:


#! usr/local/bin/perl 

print STDOUT "Hello\!\n";
print STDOUT "This program will take a folder of Affymetrix text files
+ and put\n";
print STDOUT "their signal data in a format useful for Cyber-T\.\n";
print STDOUT "Please enter the name and location of the directory to p
+arse\:\n";
$directory=<STDIN>;
open (OUTPUTFILE,">data.csv"); 
opendir(DIR, "$directory") or die "Failed to open $directory: $!"; 
while (defined(@filename = readdir(DIR))) { 
@spliced_data=splice(@filename, 0, 15);
foreach $_(@filename) { 
   ($a, $b, $c, $d, $e, $f)=split(/\t/);
   push(@final_data, "$d\n");} 
print OUTPUTFILE "@final_data";
}
closedir(DIR);
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Thanks for your help!!