#! /usr/bin/perl
use warnings;
use strict;
my %hash;
while(<DATA>) {
    chomp;
    my @col = split " ", $_;
    next unless exists $col[3];
    next unless $col[3] =~ /^S\d{5}GM\d{3}$/;
    my $key = substr($col[3],1,5);
    push @{$hash{$key}} , [ @col ]; 
}

for ( sort keys %hash ) {
   my $i = $_;
   $i =~ s/^0+//g;
   my $file = "output_$i.txt";
#   open FILE, ">", "$file" or
#       die("Cannot open file $file\n");
   print "FILE: $file\n";
   for my $col ( @{$hash{$_}} ) {
       print join (" ", @$col), "\n";
#       print FILE join (" ", @$col), "\n";

   }	   
#  close (FILE);
}


__DATA__
11880    13417    -    S00010GM001    sml_056    sp|YV02233      desc
13804    14685    -    S00010GM002    sml_045    sp|YV02643      desc
15525    18026    -    S00001GM001    sml_032    sp|V023334      desc
32763    34239    +    S00002GM001    sml_028    sp|YV02376      desc
67929    68933    -    S00003GM001    sml_025    sp|YV02346      desc
90562    91368    +    S00012GM001    sml_025    sp|YV02376      desc
10209    10433    -    S00012GM002    sml_046    sp|YV02355      desc
12522    12576    +    S00013GM001    sml_027    sp|0235777      desc
13247    13349    -    S00013GM002    sml_088    sp|YV02375      desc

##</code><code>##

C:\Perl>perl onfour.pl
FILE: output_1.txt
15525 18026 - S00001GM001 sml_032 sp|V023334 desc
FILE: output_2.txt
32763 34239 + S00002GM001 sml_028 sp|YV02376 desc
FILE: output_3.txt
67929 68933 - S00003GM001 sml_025 sp|YV02346 desc
FILE: output_10.txt
11880 13417 - S00010GM001 sml_056 sp|YV02233 desc
13804 14685 - S00010GM002 sml_045 sp|YV02643 desc
FILE: output_12.txt
90562 91368 + S00012GM001 sml_025 sp|YV02376 desc
10209 10433 - S00012GM002 sml_046 sp|YV02355 desc
FILE: output_13.txt
12522 12576 + S00013GM001 sml_027 sp|0235777 desc
13247 13349 - S00013GM002 sml_088 sp|YV02375 desc