Yes, I guess a s/\r\n/\n/g followed by chomp would do it:

$ cat unixordos.pl
use strict;
use warnings;
my $fh = undef;
open($fh, "<", "foo.txt") or die "failed to open 'foo.txt':$!";

while (my $line = <$fh>) {
  $line =~ s/\r\n/\n/g;
  chomp $line;
  ($line =~ m/^\d+$/)
    ? print qq{number ok:"$line"}
    : print qq{number error:"$line"};
  print "\n";
}
close($fh) or die "failed to close 'foo.txt':$!";
__END__
$ echo -e "123\n456\n789" > foo.txt
$ perl unixordos.pl
number ok:"123"
number ok:"456"
number ok:"789"
$ unix2dos foo.txt
unix2dos: converting file foo.txt to DOS format ...
$ perl unixordos.pl
number ok:"123"
number ok:"456"
number ok:"789"
$
[download]

Will this work generally?