Thanks grandfather,

I think I confused everyone. As you indicated there are 10 columns and I am working with the forth and the ninth (index 3 and 8). This code does not work unless I remove the comment form "# push(@genes_number, $current_line[ 1 ]);" and comment "push(@{$genes_number{$k}}, $current_line [ 1 ]);"

Here is the complete code that reads the first file and store the data into the %gc_ag. In the data section I have included the first few rows of first file and the second file. 

#!/usr/bin/perl -w

use strict;
use warnings;
use File::Path;
use vars qw(@genes_number %count $AG_value $GC_bin @arr %gc_ag);
######################################################################
+###############
#                         Open Input and Output Files                 
+              #
######################################################################
+###############
if( @ARGV < 2){

      print "NSD analysis file needs the following arguments\n";
      print "Name of merged Static and experimental file, Name of expe
+riment (first col of first file, Output file name\n";
      exit 0;
}
opendir (DIR, "/nsd/data") || die "Cannot open directroy data $!";
open(NSD, "firstfile.txt") || die "Cannot open file NSD file"; # NSD d
+ata
open(INPUT1,$ARGV[0]) || die "Cannot open file \"$ARGV[0]\""; # Analys
+is file
my $exp_name=$ARGV[1] || die "Enter the name of Experiment \"$ARGV[1]\
+"";
open(RESULTS, ">/nsd/data/$ARGV[2]")|| die "Cannot open the results fi
+le";
#my $GC_bin=$ARGV[3] || die "Enter the GC content that you want to anl
+yze \"$ARGV[2]\"";

#open(RESULTS,">result.txt")|| die "Cannot open the results file";
#my $AG_value=0;
# read all AG 90 values for all gc bins into  a hash
# then for the keys of this hash use the values for making # compariso
+ns

my %gc_ag =();
while(<NSD>){
         chomp;
          my @current_line_nsd  = split /\t/;
            if ($exp_name eq $current_line_nsd[0]){
                       $gc_ag{$current_line_nsd[2]} = $current_line_ns
+d[17];

           }
    }

         foreach my $v (sort {$a<=>$b} keys %gc_ag) {
         print "$v\t$gc_ag{$v}\n";
         }

close (NSD);

#reading the second file entered by user as an argument
my %genes_number =();
while(<INPUT1>){
         chomp;
          my @current_line  = split /\t/;

          foreach my $k (sort {$a<=>$b} keys %gc_ag) {

                if ($current_line[3] == $k && $current_line[8] > $gc_a
+g{$k} ) {

          # push(@genes_number, $current_line[1]);

          push(@{$genes_number{$k}}, $current_line[1]);
          }
     }
}

&count_unique (@genes_number);


######################################################
sub count_unique {

     @genes_number = @_;

     my %count;

     map { $count{$_}++ } @genes_number;

      #print them out:

     map {push our @arr, ${count{$_}}} sort keys(%count);


     for (my $j=1; $j<10; $j++){
     my $counter =0;
         foreach my $element(@arr) {

                   if ($element >=$j) {
             $counter++;
        }
     }
     print "$j\t$counter\n";
}
     #print "Number of genes with more than 5 probes is: $counter\n";
     #print scalar(@arr)."\n" ;
     #map {print RESULTS "$_\n"} sort keys(%count);
     my $i =0;
         $i += keys %count;
        # print $i;

     return %count;
}

close (INPUT1);
close (RESULTS);
close (DIR);

[download]

THE FIRST FILE 

PEPG_GT1001_01_HYB1_N   2008-06-26      5       1406    1163    2.2748
+3 2.66979 2.77429 2.91807 3.10535 3.24583 3.24583 3.43355 3.67937 3.9
+0971 4.51388 4.88935 5.33778 6.30833 38.3232 2.27483 2.77429 2.91807 
+3.10535 3.24583 3.43355 3.67937 4.22568 4.51388 5.33778 7.52172 9.753
+74 14.9343 27.3547 922.32
PEPG_GT1001_01_HYB1_N   2008-06-26      6       1746    65825   2.3526
+1 2.77429 2.91807 2.91807 3.10535 3.24583 3.43355 3.67937 3.67937 4.2
+2568 4.51388 4.88935 5.67276 6.81457 72.5727 2.20176 2.91807 3.10535 
+3.24583 3.43355 3.90971 4.51388 5.33778 6.81457 9.75374 15.8048 22.22
+25 34.325  60.0727 2805.0
PEPG_GT1001_01_HYB1_N   2008-06-26      7       1828    356967  2.2748
+3 2.66979 2.91807 2.91807 3.10535 3.24583 3.43355 3.67937 3.90971 4.2
+2568 4.88935 5.33778 6.30833 8.14622 58.5727 2.14818 3.10535 3.43355 
+3.67937 4.22568 5.33778 6.81457 9.75374 14.9343 23.4265 38.3232 50.32
+27 69.5727 114.323 4083.8
PEPG_GT1001_01_HYB1_N   2008-06-26      8       1880    747766  2.2748
+3 2.77429 2.91807 3.10535 3.10535 3.24583 3.67937 3.90971 4.22568 4.5
+1388 5.33778 6.30833 7.52172 10.767  176.073 2.14818 3.43355 3.90971 
+4.88935 5.67276 9.75374 15.8048 24.8939 36.8235 53.3227 74.8227 92.57
+27 121.073 185.323 13073.
PEPG_GT1001_01_HYB1_N   2008-06-26      9       1918    1068262 2.2748
+3 2.77429 2.91807 3.10535 3.24583 3.43355 3.67937 3.90971 4.51388 4.8
+8935 6.30833 6.81457 9.11957 12.5488 131.823 2.14818 3.90971 5.33778 
+7.52172 11.6325 22.2225 35.574  50.3227 68.3227 91.0727 123.823 147.8
+23 185.323 274.073 7170.9
PEPG_GT1001_01_HYB1_N   2008-06-26      10      1904    1212972 2.3526
+1 2.91807 3.10535 3.24583 3.43355 3.67937 4.22568 4.51388 5.33778 6.8
+1457 9.11957 11.6325 15.8048 24.8939 1374.32 2.20176 4.88935 8.14622 
+14.9343 23.4265 40.8228 61.5727 81.8227 105.073 133.073 174.573 204.3
+23 252.573 365.823 20092.
PEPG_GT1001_01_HYB1_N   2008-06-26      11      1920    1128925 2.4355
+6 2.91807 3.24583 3.43355 3.67937 4.22568 4.88935 5.33778 6.81457 9.1
+1957 13.9124 18.4569 26.1208 40.8228 356.073 2.20176 6.30833 12.5488 
+24.8939 36.8235 61.5727 85.8227 111.573 141.073 176.073 224.323 259.5
+73 316.073 449.073 8523.3
PEPG_GT1001_01_HYB1_N   2008-06-26      12      1946    864327  2.3526
+1 3.10535 3.43355 3.67937 4.22568 4.88935 5.67276 7.52172 9.75374 14.
+9343 22.2225 30.3334 40.8228 62.8227 681.073 2.27483 8.14622 19.6077 
+34.325  49.0727 79.0727 107.573 138.573 172.323 212.323 267.323 307.8
+23 371.073 521.323 8956.5
PEPG_GT1001_01_HYB1_N   2008-06-26      13      1936    550147  2.4355
+6 3.43355 3.67937 4.22568 4.88935 6.30833 8.14622 10.767  14.9343 22.
+2225 34.325  43.8227 64.3227 96.8227 696.323 2.27483 10.767  26.1208 
+42.0728 58.5727 91.0727 123.823 157.323 193.573 238.073 298.573 342.8
+23 411.323 580.073 9509.3
PEPG_GT1001_01_HYB1_N   2008-06-26      14      1920    291085  2.5241
+8 3.67937 4.22568 4.88935 5.67276 8.14622 11.6325 15.8048 23.4265 32.
+5776 50.3227 61.5727 79.0727 116.823 797.823 2.35261 13.9124 30.3334 
+46.3227 62.8227 96.8227 130.323 166.573 205.823 252.573 318.573 367.0
+73 445.073 635.823 9819.0
PEPG_GT1001_01_HYB1_N   2008-06-26      15      1898    126329  2.3526
+1 3.67937 4.51388 5.33778 6.81457 9.75374 15.8048 22.2225 32.5776 45.
+0727 64.3227 81.8227 111.573 174.573 1178.57 2.52418 15.8048 31.3308 
+48.0727 62.8227 95.3227 129.073 166.573 207.323 258.323 328.073 383.0
+73 470.573 708.323 8939.0
PEPG_GT1001_01_HYB1_N   2008-06-26      16      1926    45400   2.6697
+9 4.22568 5.67276 7.52172 9.11957 13.9124 21.0305 30.3334 40.8228 58.
+5727 83.0727 100.823 130.323 191.073 1184.07 2.52418 15.8048 32.5776 
+48.0727 62.8227 92.5727 126.323 162.573 204.323 259.573 341.323 406.0
+73 517.323 833.823 9437.3
PEPG_GT1001_01_HYB1_N   2008-06-26      17      1884    12459   2.7742
+9 4.88935 6.30833 8.14622 10.767  17.1358 26.1208 36.8235 49.0727 66.
+8227 98.0727 119.823 157.323 245.823 1871.82 2.66979 17.1358 31.3308 
+45.0727 60.0727 90.0727 121.073 159.823 205.823 267.323 368.323 454.3
+23 615.573 1013.32 9156.5
PEPG_GT1001_01_HYB1_N   2008-06-26      18      1824    1925    2.7742
+9 5.33778 7.52172 9.75374 12.5488 19.6077 29.0895 40.8228 53.3227 76.
+3227 106.323 134.323 181.573 302.573 2503.57 3.43355 15.8048 29.0895 
+42.0728 56.0727 80.5727 114.323 157.323 205.823 279.823 407.323 537.5
+73 760.073 1567.82 8010.4
PEPG_GT1001_01_HYB2_N   2008-06-26      5       1406    1163    2.2748
+3 2.66979 2.77429 2.8588  2.97936 3.10535 3.20743 3.39102 3.5525  3.9
+0971 4.16394 4.63902 5.33778 6.95136 43.8227 2.35261 2.8588  2.97936 
+3.10535 3.20743 3.5525  3.72086 4.445   4.97054 6.11439 8.71517 10.76
+7  16.8886 31.3308 684.57
PEPG_GT1001_01_HYB2_N   2008-06-26      6       1746    65825   2.2748
+3 2.66979 2.8588  2.97936 2.97936 3.10535 3.39102 3.5525  3.72086 4.1
+6394 4.63902 4.97054 5.67276 6.95136 70.8227 2.21903 2.8588  3.10535 
+3.20743 3.5525  3.90971 4.445   5.33778 6.95136 10.0787 16.8886 22.94
+34 34.325  59.5727 3348.5
PEPG_GT1001_01_HYB2_N   2008-06-26      7       1828    356967  2.2748
+3 2.77429 2.8588  2.97936 3.10535 3.20743 3.39102 3.5525  3.90971 4.4
+45   4.97054 5.33778 6.5127  8.14622 191.073 2.14818 3.10535 3.39102 
+3.72086 4.16394 4.97054 6.5127  9.30877 14.9343 22.9434 37.8233 49.32
+27 67.8227 109.323 4133.0
PEPG_GT1001_01_HYB2_N   2008-06-26      8       1880    747766  2.3526
+1 2.77429 2.8588  2.97936 3.10535 3.39102 3.5525  3.90971 4.16394 4.6
+3902 5.67276 6.5127  8.14622 11.4116 202.823 2.21903 3.39102 3.90971 
+4.63902 5.67276 9.30877 14.9343 23.9123 35.574  50.3227 72.5727 90.07
+27 117.323 178.573 5673.5

THE SECOND FILE


4750739 A209.EF064282   53      11      0.474968        -33.2   S     
+  4750739 165.834 44.7
3383536 A209.EF064282   55      11      0.500083        -32.4   A     
+  3383536 323.299 49
2634649 A209.EF064282   57      10      0.394855        -32     S     
+  2634649 335.989 70.8
2923929 A209.EF064282   59      10      0.440602        -32.6   A     
+  2923929 182.191 56.2
4872947 A209.EF064284   55      9       0.320984        -32.8   A     
+  4872947 532.385 103.7
1427589 A209.EF064284   57      9       0.402661        -32.2   S     
+  1427589 677.757 199.3
3642671 A209.EF064284   87      8       0.376187        -30.4   A     
+  3642671 180.485 65.7
1042210 A209.EF064284   89      7       0.320542        -29.3   S     
+  1042210 363.54  61.7
4959298 A209.EF064284   91      9       0.462034        -30.5   A     
+  4959298 549.485 105.1
2609177 A209.EF064284   93      8       0.287848        -29.9   S     
+  2609177 223.687 48
3121652 A209.EF064284   95      9       0.447002        -30.8   A     
+  3121652 491.059 104.1
4911506 A209.EF064284   97      9       0.371932        -30.2   S     
+  4911506 99.0901 24.5
4389484 A209.EF064284   99      10      0.48621 -32.2   A       438948
+4 123.912 47.2

[download]

In reply to Re^2: Print Uniqe elements of arry of hash by sesemin
in thread Print Uniqe elements of arry of hash by sesemin

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