#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11146491;showspoiler=11146492-1
use warnings;
use List::AllUtils qw( zip_by sort_by nsort_by );

my @matrix = (
    [qw/ t1 t1 t2 t2 t1 t2 /],
    [qw/ a1 a2 a1 a2 a3 a3 /],
    [qw/ mis mis mis mis del del /],
);

my @alleles_origin = qw( a2 a1 a3 );
my %alleles_sort_order = zip_by { @_ } \@alleles_origin, [ 1 .. @alleles_origin ];

my @effects = map $_->[2],
  my @sorted_transpose =
    sort_by { $_->[0] } # the tN
    nsort_by { $alleles_sort_order{ $_->[1] } } # the aN
    zip_by { [ @_ ] } @matrix;
use Data::Dump 'dd'; dd { 'sorted_transpose' => \@sorted_transpose,
  'wanted effects' => \@effects,
  'matrix' => \@matrix };

##</code><code>##

{
  "matrix" => [
    ["t1", "t1", "t2", "t2", "t1", "t2"],
    ["a1", "a2", "a1", "a2", "a3", "a3"],
    ["mis", "mis", "mis", "mis", "del", "del"],
  ],
  "sorted_transpose" => [
    ["t1", "a2", "mis"],
    ["t1", "a1", "mis"],
    ["t1", "a3", "del"],
    ["t2", "a2", "mis"],
    ["t2", "a1", "mis"],
    ["t2", "a3", "del"],
  ],
  "wanted effects" => ["mis", "mis", "del", "mis", "mis", "del"],
}