#!/usr/bin/perl
use strict;
use warnings;

open(FH,"input.txt")or die "can not open input file\n";
while (my $line=<FH>) {
    my (undef, undef, undef, $four, undef) = split("\t",$line);
    if ($four=~m/S(\d+)GM/){
        my $F = get_file_handle($1);
        print $F $line;
    }
}

##</code><code>##

my %FHList;  # Holds file handles we've opened so far
sub get_file_handle {
    my $key = shift;
    if (!exists $FHList{$key}) {
        open $FHList{$key}, '>', "output_$key.txt" or die $!;
    }
    return $FHList{$key};
}