JaeDre619:

Well both scripts are simple enough to include the second one inside the while loop of the first one, something like this:

# from second file
use strict;
use Digest::MD5 qw(md5_hex);
# from first file
my $target_dir = "/backups/test/";
opendir my $dh, $target_dir or die "can't opendir $target_dir: $!";
while (defined(my $file = readdir($dh))) {
    next if ($file =~ /^\.+$/);
    #Get filename attributes
    if ($file =~ /^foo(\d{3})\.name\.(\w{3})-foo_p(\d{1,4})\.\d+.csv$/
+) {
      print "$1\n";
      print "$2\n";
      print "$3\n";
    }
    print "$file\n";

    # From second file
    #Create new file
    open (NEWFILE, ">/backups/processed/foo$1.name.$2-foo_p$3.out")
      || die "cannot create file";
    my $data = '';
    my $line1 = <>;
    chomp $line1;
    my @heading = split /,/, $line1;
    my ($sep1, $sep2, $eorec) = ( "^A", "^E", "^D");
    while (<>)
        {
        my $digest = md5_hex($data);
        chomp;
        my (@values) = split /,/;
        my $extra = "__mykey__$sep1$digest$sep2" ;
        $extra .= "$heading[$_]$sep1$values[$_]$sep2" for (0..scalar(@
+values));
        $data .= "$extra$eorec"; 
        print NEWFILE "$data";
    }
    #print $data;
    close (NEWFILE);

# and back to the first file
}
[download]

Note: I didn't change anything except moved a couple of blocks of code (marked) and changed the indentation (should be clear enough). You'll have to make any fixes.

Rather than that, though, I think I'd just make the second script a subroutine, and call it from the first script. Again, something like the following. (Again, I'm not changing anything, just arranging stuff.):

# from second script
use strict;
use Digest::MD5 qw(md5_hex);

# from first script
my $target_dir = "/backups/test/";
opendir my $dh, $target_dir or die "can't opendir $target_dir: $!";
while (defined(my $file = readdir($dh))) {
    next if ($file =~ /^\.+$/);
    #Get filename attributes
    if ($file =~ /^foo(\d{3})\.name\.(\w{3})-foo_p(\d{1,4})\.\d+.csv$/
+) {
      print "$1\n";
      print "$2\n";
      print "$3\n";
    }
    print "$file\n";

    # New line added: call the routine to process file
    process_file($file);
}

# New line: tell perl that we're making a subroutine
sub process_file {
    # Need to get arguments here:
    my ($filename) = @_;

    # from second script
    #Create new file
    open (NEWFILE, ">/backups/processed/foo$1.name.$2-foo_p$3.out")
      || die "cannot create file";
    my $data = '';
    my $line1 = <>;
    chomp $line1;
    my @heading = split /,/, $line1;
    my ($sep1, $sep2, $eorec) = ( "^A", "^E", "^D");
    while (<>)
    {
        my $digest = md5_hex($data);
        chomp;
        my (@values) = split /,/;
        my $extra = "__mykey__$sep1$digest$sep2" ;
        $extra .= "$heading[$_]$sep1$values[$_]$sep2" for (0..scalar(@
+values));
        $data .= "$extra$eorec"; 
        print NEWFILE "$data";
    }
    #print $data;
    close (NEWFILE);
}
[download]

Oh, yes, you asked for some best practice suggestions, too. The only ones that jump out at me are:

• Use the three argument form of open, like this:
  

      open (NEWFILE, ">", "/backups/processed/foo$1.name.$2-foo_p$3.out"
  +)
  [download]

  it has the advantage of being safer. In some cases (such as the one here the filename can be executed by the operating system. If the string is provided by the user, they could cause you some serious problems. With the three argument form, you're safe from that: perl treats the string as a filename and doesn't try to execute it.
• If you use the lower precedence or operator, you can omit the parenthesis on your open statement, like this:
  

      open NEWFILE, ">", "/backups/processed/foo$1.name.$2-foo_p$3.out"
        or die "cannot create file";
  [download]

Update: Added readmore tags and best practice suggestions.

Is this the kind of suggestion you were seeking?

...roboticus

When your only tool is a hammer, all problems look like your thumb.