... I will assume your Regular file will contain the dashes.

Actually, it appears to be the other way around. And here's an even simpler way (no need to split): 

#!/usr/bin/perl

use strict;
use warnings;

my @filenames = qw/Reg Irreg/;
my %ofh =
    map { open( my $fh, ">", $_.'ularOlios.txt' ) or die $!; $_ => $fh
+ }
        @filenames;

while (<DATA>) {
    my $o = ( /^\w+-/ ) ? $ofh{Irreg} : $ofh{Reg};
    print $o $_;
}
close $_ for ( values %ofh );

__DATA__
10002TU    AGACATTACCTGTGAGACACCTTTC GCCTCCACCTCAGAGTCAG      TCCATGGG
+AAGGATCTCCGTGAAATCA
10002TU-2  GCTCCAGCTAGAAGAGAATCC     CCCACCAGGGCTGTGTAAG      CCTGTGAG
+ATAGTACAGCTGAAGAGTTGGC
10002TD    TGTGTTGATTCTCAGCCTCTTG    GACGGAGCACATAGGCAAAG     TCTGTTCT
+TCTCAGCTGTCTTTGTTGCTGC
10003TU    CAGCAAGCCCTGAGGTGTG       CAGTGAACTGAGAAAGACGAGAGG TGCAAGTC
+CAGATGGAGGCCACC
10174TU-2  ACCTGAACAGCCTGACATGAAC    TGGGATGGAGGGCAAAGTC      CCACCTAG
+TATGACCCAGCACACCTCC

[download]

In reply to Re^2: separate data and print to two files by graff
in thread separate data and print to two files by lomSpace

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.