How do you compare two columns of data and print the results. The values in one column is repeated so i want to compare with another column and print only once those values that match. 
#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Std;
my $file = "lethal_results2.txt"; # input file containing nubiscan res
+ults
my $ge = "geneid.txt"; # file with TE name and length
open(FILE,"<",$file) or die("Unable to open file $file: $!");
open(GE,"<",$ge) or die("Unable to open $ge: $!");
my @file_data = <FILE>;
my @ge_data = <GE>; #input stored in an array
close(FILE);
close(GE);
foreach my $line (@ge_data) 
{
    my @line = split(/\s+/,$line); 
    my $start = $line[0];
    #print"$line[0] \n";
    foreach my $values(@file_data)  
    {
        my @values = split(/\s+/, $values);
        my $id = $values[0];
        #print"$values[0] \n";
        my $width = 11;
        if ($values[0] eq $line[0]) 
        {
            #print"the gene id \n";
            print"$line[0] \n";
        }
    }
}

[download]
This code prints all the values just as it is split does not compare and print them as i want it.. The column1 data: 
ENSMUSG00000050310
ENSMUSG00000025583
ENSMUSG00000021198
ENSMUSG00000052595
ENSMUSG00000015243
ENSMUSG00000024130
ENSMUSG00000031333
ENSMUSG00000026842
ENSMUSG00000026596
ENSMUSG00000020532
ENSMUSG00000026003
ENSMUSG00000023328
ENSMUSG00000029580
ENSMUSG00000054808
ENSMUSG00000026836

[download]
Column 2: 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000050310 
ENSMUSG00000025583 
ENSMUSG00000025583 
ENSMUSG00000025583 
ENSMUSG00000025583 
ENSMUSG00000025583

[download]
In the second column the values are repeated so i want to compare the values in both columns and then print those present in both only once without repetition.

In reply to Comparing two columns by Nalababu

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