The simplest way to overcome the problem you encounter is to count the number of fields in @$col and handle the last few terms separately.

#! /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{$_}} ) {
       my $col_count = scalar @$col - 1;
       if ( $col_count > 6 ) {
           #
           # use array slices to partition data.
           #
           my $end = join " ", @$col[6..$col_count];
           my $begin = join "\t", @$col[0..5];
           print $begin, "\t", $end, "\n";
       }          
       else {
           print join ("\t", @$col), "\n";
       }
#       replace prints with print FILE etc.

   }       
#  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 
+not found
90562    91368    +    S00012GM001    sml_025    sp|YV02376      desc 
+not found
10209    10433    -    S00012GM002    sml_046    sp|YV02355      desc
12522    12576    +    S00013GM001    sml_027    sp|0235777      desc
13247    13349    -    S00013GM002    sml_088    sp|YV02375      desc

[download]
The output is:

C:\Code>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 n
+ot found
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 n
+ot found
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

[download]

In reply to Re^3: segregating data from one file to many files by dwm042
in thread segregating data from one file to many files by patric

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