thanks for all the suggestions, and yes the output should look like the output that anonymous monk posted above.

I can read the file into an array, but I wasn't sure how to proceed through the array to average columns 6 and 7.

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long;

my $infile;
my @fields;
my $i;
my $j;

GetOptions (
        "infile=s" => \$infile,
);


open INFILE, "<$infile" or die $!;
#open RES, ">result.txt" or die $!;

while (<INFILE>){



        @fields = split(/\t+/, $_);
        my ($name, $chr, $location, $gen, $dom, $pval, $fst) = @fields
+[0..6];

}
[download]

once I have my values in an array, how do I find average of all similar values for column 3? eg how do I find all of those that have 34.9 and average the result in column 6?

Please explain in words, how you would do it, using paper and pencil

well I've written something that almost does the job, except it goes wrong on the very last line of the file. I read the file into an array and calculate the averages which I then put into a hash and then iterate through the array and lookup values from the hashes. I'm sure there's a more elegant way to do it though....

#!/usr/bin/perl

# Usage: perl average_table.pl -i <input file>
use strict;
use warnings;
use Getopt::Long;
my $infile;
my @fields;
my @array;
my @values;
my %hash;
my $add_fst;
my @out;
my @count;
my $i=1;
my @final;
my %pval;
my %fst;

                my $prev_loc;
                my $prev_pval;
                my $prev_fst;
        my $prev_join;

GetOptions (
        "infile=s" => \$infile,
);


open INFILE, "<$infile" or die $!;
@fields = <INFILE>;
foreach (@fields){

        @array = split(/\t+/, $_);
        chomp (@array);
        my ($name, $chr, $location, $gen, $dom, $pval, $fst) = @array[
+0..6];
        my $join = "$chr-$location";
        push (@values, $join, $pval);

            if ($location == $prev_loc){
            $pval = $pval + $prev_pval;
            $fst = $fst + $prev_fst;
            $i++;
            }    

            elsif ($location != $prev_loc) { 
            my $pval_average = ($prev_pval / $i);
            my $fst_average = ($prev_fst / $i);
            my $join2 = "$prev_join\t$pval_average\t$fst_average";
            $pval{$prev_join} = $pval_average;
            $fst{$prev_join} = $fst_average;        
            push (@final, $join2);
            $i = 1;
            } 
        
        $prev_loc = $location;
        $prev_pval = $pval;
        $prev_fst = $fst;
        $prev_join = $join;
    }


foreach (@fields){
            @out = split(/\t+/, $_);
            chomp (@out);
            my ($name, $chr, $location, $gen, $dom, $pval, $fst) = @ou
+t[0..6];
                my $join = "$chr-$location";
        my $new_pval = $pval{$join};
        my $new_fst = $fst{$join};

        print $name."\t".$chr."\t".$location."\t".$gen."\t".$dom."\t".
+$new_pval."\t".$new_fst."\n";
        }
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