Firstly, when posting example code, please use "code" tags, as described in Writeup Formatting Tips. This makes it easier for others to understand and download your code.

Secondly, it would have been better to create a more meaningful title for the posting: "Simple or not" conveys no useful meaning.

Now, on to (what I think is) your problem. If you are trying to replace all whitespace in your input with tabs, then preserve the newline, the following should accomplish that task (untested):

use strict;
use warnings;

open my $fh_in , '<', 'test1.txt' or die "Can not open file test1.txt:
+ $!";
open my $fh_out, '>', 'test2.txt' or die "Can not open file test2.txt:
+ $!";
while (<$fh_in>) {
    s/\s+/\t/g;    
    print $fh_out "$_\n";
}
close $fh_out;
close $fh_in;
[download]

In my opinion, you never clearly stated what your goal was. It would have been more useful if you had supplied a few sample lines of your input file, your actual output and your expected output.

The most efficient way to squash (convert multiple characters to a single instance) is to use tr///s:

$line =~ tr/ /\t/s;
[download]

I do have problems with the last \s since I need my \n

Maybe you could explicitly match spaces in the replacement (instead of whitespace). Or chomp off the newline first and then append it back on when you're done with the whitespace -> tab substition.  If I understood the problem correctly, that is...

First, please read Writeup Formatting Tips, as wrapping your code in <code> tags would dramatically improve the formatting.

Rather than rolling your own, I'd recommend using Text::CSV and setting the sep_char attribute to a space, a la:

my $csv = Text::CSV->new({sep_char => ' '});

Your regular expression: $line =~ s/ s{2,}/\t/s is converting " ss" and " ssss" to tabs and it is only converting the first one because you don't have a global flag at the end. To replace the tabs you would need s/\s\s+/\t/g or s/\s{2,}/\t/g. Note the backslash before the "s".

As for keeping the final newline, I would recommend stripping it before you apply the regex and adding it after you are done. There are ways to do that with regular expressions alone but your regular expression would be quite complicated. So the code to prep the line should look something like this:

while(my $line = <FH>) {
   #strip newline
   chomp $line;

   #replace runs of two or more spaces with tabs
   $line =~ s/\s\s+/\t/g;

   #add back newline
   $line .= "\n";

   #.... do whatever with $line ....
}
[download]

Best, beth

open my $fh_in , '<', 'test1.txt' or die "Can not open file test1.txt:
+ $!";
open my $fh_out, '>', 'test2.txt' or die "Can not open file test2.txt:
+ $!";
while (<$fh_in>) {
    s/\s+/\t/g;    
    print $fh_out "$_\n";
}
close $fh_out;
close $fh_in;
[download]

MGI:1918918                    381629                         0610007C
+21Rik             5            syntenic            51374             
+             C2orf28                   2p23.3                    B
MGI:1918917                    71667                          0610007L
+01Rik             5            syntenic F          55069             
+             C7orf42                   7q11.21                   C
MGI:1923501                    76251                          0610007P
+08Rik             13           syntenic B3         375748            
+             C9orf102                  9q22.32                   M
MGI:1915571                    58520                          0610007P
+14Rik             12           syntenic            11161             
+             C14orf1                   14q24.3                   B
[download]

Your issue here arises from the fact you are starting with a fixed-width file, not a white-space delimited file - the latter cannot contain a null column with its body by construction.

You can roll your own solution using substr or pack/unpack. However, it's probably a good idea to turn to CPAN and use one of the many fixed width parsing modules available (e.g. search terms fixedwidth, fixedlength).

Update: You reposted the problem outside this thread here. You shouldn't break threads unnecessarily, and you really shouldn't double post.