I'm trying to write a little program that will ultimately weed out blast hits that are too similar. The idea is to have it read in a tab-delimited line of data, then split it up into an array and do the same for the next line of data. If the first columns are the same for both lines (arrays), push the array to another array, looping through until we have an array of arrays that have the same first column value. Then I'd like to compare the values in the 2nd column of the arrays in that array. If they are equal, we don't need to do anything, but if they are different, then the values in the second-to-last column must have a difference of 10. Here is the code so far (doesn't work yet): 

use strict;
use warnings;

open(input0, "<e_d.txt");
open(output0, ">e_h.txt");

my $colNum=0;
my $limit=10;
my @arrayEquals;

my $line = <input0>;

WHILE: while($line ne undef) { 

    s/\r?\n//;
    my @array = split /\t/, $line; 

    my $followingLine = <input0>;
    my @followingLineArray=split /\t/, $followingLine;

    if( $array[$colNum] eq $followingLineArray[$colNum]){
        print "match\n";
        push (my @arrayEquals, @array);
    }
    else{
        push (@arrayEquals, @array);
        for my $i(0 .. $#arrayEquals){
            my $colNum=1
            if ($arrayEquals[$i][$colNum] eq $arrayEquals[$i+1][$colNu
+m]){
                next;
            }else{
                my $colNo=-2;
                if (($arrayEquals[$i][$colNo] - $arrayEquals[$i+1][$co
+lNo]) < $limit) { #not enough difference so won't keep any of the lin
+es in @arrayEquals
                    $line = $followingLine;
                    next WHILE;
                }
            }
        }
            print output0 @arrayEquals; #has difference, so keep the v
+alues
        $line = $followingLine;
    }
}

[download]

So for example, say I get to this part of my data (some column removed for simplicity):

KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.1    2e-139     497
KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.1    4e-46     187
KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.2    4e-46     187

[download]

I'd be trying to compare IMGA|Medtr4g125100.1-> 2e-139 and IMGA|Medtr4g125100.2-> 4e-46 (false positive) and then IMGA|Medtr4g125100.1-> 4e-46 IMGA|Medtr4g125100.2-> 4e-46 (not a difference of 10 so throw them all out) So far accessing the 2D arrays correctly are giving me trouble, but I think my bigger question and the reason for all the explanation would be that I feel like I'm not using everything perl has to offer, because I just don't know enough. So I was also wondering if there is a better way to do this. Thanks for any input

In reply to Accessing 2D array values and comparing by mSe

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