How to delete a specific array in an array of array references?

Question

I am interested in deleting a specific array from an array of array references. Towards this end I loop through the array references and look for a match. If a match is found, I attempt to delete this specific array reference by setting it to equal nothing. There are two strange things that happen in the script that I have written: 1) The code seems to identify the presence of a match between the array of interest and an array reference, even before the array reference that matches it is processed. 2) In trying to delete one specific array reference, I end up deleting all of them. Here is my code:

#!/usr/bin/perl
use strict;
use warnings;

my @array_1 = ('CTCTTGCCTCAATCATATAT', 'CTCTTGCCTCATTGATATAT', 'CTCTTGCCTCAATCATATAT', 'CACTTGCCTCAATGAAATTT', 'GTCTTGCCTCATTGATAAAT', 'CACTTGCCTCAATGTAATAT', 'CTCTTCCCTCAATGATTTAA', 'CACTTGCCTCAATGATATAT', 'CTCTTGCCTCATTGATATAT', 'CTCTTGCCTCAATGTTATAT', 'CTGATGCCTCATTGATATAT', 'CTGTTGGCTCAATCATATAT');
my @array_2 = ('CACTTGCCTCAATGTAATAT', 'TATCATTGCCCAATTTAAGT', 'CACTTGCCTCAATGATATAT', 'CTCTTCCCTCAATGATTTAA', 'CTCTTGCCTCAATGTTATAT', 'CTGTTGGCTCAATCATATAT', 'CTGATGCCTCATTGATATAT', 'GTCTTGCCTCATTGATAAAT', 'CACTTGCCTCAATGAAATTT');
my @array_3 = ('TATCATTGCCCAATTTAAGT', 'TTTCTTTGCCGAATATAAGT', 'TTTCTATGCGCAATTTAAGT', 'TATCTTAGCCCAATTTTTGT', 'TTTCTTTGCCCAATATATGT', 'TTTCTTTGGCCTATTTTTGT', 'TTTGTTTGGCCATTTTATGT', 'TTTCTTTGGCGAATTTATCT', 'TTTCATTGCCCAATTATTGT', 'TTTCTTTGCCCAAAATAAGT', 'CACTTGCCTCAATGTAATAT');
my @array_4 = ('TTTCTTTGCCCAATATATGT', 'TTTCTTTGCCGAATATAAGT', 'TTTCTATGCGCAATTTAAGT', 'TATCTTAGCCCAATTTTTGT', 'TTTCTTTGGCCTATTTTTGT', 'TTTGTTTGGCCATTTTATGT', 'TTTCTTTGGCGAATTTATCT', 'TTTCATTGCCCAATTATTGT', 'TATCATTGCCCAATTTAAGT', 'TTTCTTTGCCCAAAATAAGT', 'CTCTTGCCTCAATCATATAT');

my $array_1_ref = \@array_1;
my $array_2_ref = \@array_2;
my $array_3_ref = \@array_3;
my $array_4_ref = \@array_4;

my @array_to_delete = ('CACTTGCCTCAATGTAATAT', 'TATCATTGCCCAATTTAAGT', 'CACTTGCCTCAATGATATAT', 'CTCTTCCCTCAATGATTTAA', 'CTCTTGCCTCAATGTTATAT', 'CTGTTGGCTCAATCATATAT', 'CTGATGCCTCATTGATATAT', 'GTCTTGCCTCATTGATAAAT', 'CACTTGCCTCAATGAAATTT');
print "Array to delete: ", join(", ", @array_to_delete), "\n";

my @array_of_array_references = ($array_1_ref, $array_2_ref, $array_3_ref, $array_4_ref);

for (my $i = 0; $i <= $#array_of_array_references; $i++){
    print "\n", "A single array in the array of array references: ", join(", ", @{$array_of_array_references[$i]}), "\n";
    if (@array_to_delete = @{$array_of_array_references[$i]}){
            print "Both arrays match!\n";
            @{$array_of_array_references[$i]} = ();
    }
}
for (my $i = 0; $i <= $#array_of_array_references; $i++){
    print "\n", "A single array in the array of array references after removing one: ", join(", ", @{$array_of_array_references[$i]}), "\n";
}

The output is:

Array to delete: CACTTGCCTCAATGTAATAT, TATCATTGCCCAATTTAAGT, CACTTGCCTCAATGATATAT, CTCTTCCCTCAATGATTTAA, CTCTTGCCTCAATGTTATAT, CTGTTGGCTCAATCATATAT, CTGATGCCTCATTGATATAT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGAAATTT

A single array in the array of array references: CTCTTGCCTCAATCATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATCATATAT, CACTTGCCTCAATGAAATTT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGTAATAT, CTCTTCCCTCAATGATTTAA, CACTTGCCTCAATGATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATGTTATAT, CTGATGCCTCATTGATATAT, CTGTTGGCTCAATCATATAT
Both arrays match!

A single array in the array of array references: CACTTGCCTCAATGTAATAT, TATCATTGCCCAATTTAAGT, CACTTGCCTCAATGATATAT, CTCTTCCCTCAATGATTTAA, CTCTTGCCTCAATGTTATAT, CTGTTGGCTCAATCATATAT, CTGATGCCTCATTGATATAT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGAAATTT
Both arrays match!

A single array in the array of array references: TATCATTGCCCAATTTAAGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGCCCAATATATGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TTTCTTTGCCCAAAATAAGT, CACTTGCCTCAATGTAATAT
Both arrays match!

A single array in the array of array references: TTTCTTTGCCCAATATATGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TATCATTGCCCAATTTAAGT, TTTCTTTGCCCAAAATAAGT, CTCTTGCCTCAATCATATAT
Both arrays match!

A single array in the array of array references after removing one: 

A single array in the array of array references after removing one: 

A single array in the array of array references after removing one: 

A single array in the array of array references after removing one: 

Expected output:

Array to delete: CACTTGCCTCAATGTAATAT, TATCATTGCCCAATTTAAGT, CACTTGCCTCAATGATATAT, CTCTTCCCTCAATGATTTAA, CTCTTGCCTCAATGTTATAT, CTGTTGGCTCAATCATATAT, CTGATGCCTCATTGATATAT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGAAATTT

A single array in the array of array references: CTCTTGCCTCAATCATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATCATATAT, CACTTGCCTCAATGAAATTT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGTAATAT, CTCTTCCCTCAATGATTTAA, CACTTGCCTCAATGATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATGTTATAT, CTGATGCCTCATTGATATAT, CTGTTGGCTCAATCATATAT

A single array in the array of array references: CACTTGCCTCAATGTAATAT, TATCATTGCCCAATTTAAGT, CACTTGCCTCAATGATATAT, CTCTTCCCTCAATGATTTAA, CTCTTGCCTCAATGTTATAT, CTGTTGGCTCAATCATATAT, CTGATGCCTCATTGATATAT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGAAATTT
Both arrays match!

A single array in the array of array references: TATCATTGCCCAATTTAAGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGCCCAATATATGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TTTCTTTGCCCAAAATAAGT, CACTTGCCTCAATGTAATAT

A single array in the array of array references: TTTCTTTGCCCAATATATGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TATCATTGCCCAATTTAAGT, TTTCTTTGCCCAAAATAAGT, CTCTTGCCTCAATCATATAT

A single array in the array of array references after removing one: CTCTTGCCTCAATCATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATCATATAT, CACTTGCCTCAATGAAATTT, GTCTTGCCTCATTGATAAAT, CACTTGCCTCAATGTAATAT, CTCTTCCCTCAATGATTTAA, CACTTGCCTCAATGATATAT, CTCTTGCCTCATTGATATAT, CTCTTGCCTCAATGTTATAT, CTGATGCCTCATTGATATAT, CTGTTGGCTCAATCATATAT

A single array in the array of array references after removing one: TATCATTGCCCAATTTAAGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGCCCAATATATGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TTTCTTTGCCCAAAATAAGT, CACTTGCCTCAATGTAATAT

A single array in the array of array references after removing one: TTTCTTTGCCCAATATATGT, TTTCTTTGCCGAATATAAGT, TTTCTATGCGCAATTTAAGT, TATCTTAGCCCAATTTTTGT, TTTCTTTGGCCTATTTTTGT, TTTGTTTGGCCATTTTATGT, TTTCTTTGGCGAATTTATCT, TTTCATTGCCCAATTATTGT, TATCATTGCCCAATTTAAGT, TTTCTTTGCCCAAAATAAGT, CTCTTGCCTCAATCATATAT

Answer 1

Code such as

if (@array_1 == @array_2)   # same number of elements?

tests whether the arrays have the same number of elements. This is because the == operator imposes the scalar context on both sides, and in scalar context an array is evaluated to return the number of its elements.

To test whether arrays are equal you need to compare their elements, with a few additional checks and refinements. As for many things in Perl, there are also modules that do that for us.

With Array::Compare for example, in its simplest usage:

use Array::Compare;

my $comp = Array::Compare->new;    
...
if ($comp->compare(\@ary1, \@ary2))  # they are equal

There is more that can be set up with the module, and there is a number of other modules for all kind of work with arrays and lists.

The code in the question also uses = (assignment!) instead of comparison ==.

With a few simplifications

use warnings;
use strict;
use Data::Dump qw(dd);  # to show complex data structures

use Array::Compare;

my $cobj = Array::Compare->new;

my @data = ( 
   ['CTCTTGCCTCAATCATATAT', 'CTCTTGCCTCATTGATATAT', ... ],
   ['CACTTGCCTCAATGTAATAT', 'TATCATTGCCCAATTTAAGT', ... ],
   ...
);

my @ary_to_del = ('CACTTGCCTCAATGTAATAT', 'TATCATTGCCCAATTTAAGT', ...);

foreach my $ra (@data) {
    @$ra = () if $cobj->compare(\@ary_to_del, $ra);
}

dd \@data;

This "empties" the anonymous arrays in @data that are equal to @ary_to_del, as code in the question does, but their array references remain in @data even as there is nothing in them.

If you were rather to remove such elements altogether then overwrite the array

@data = grep { not $cobj->compare(\@ary_to_del, $_) } @data;

instead of the foreach loop above. This uses grep to filter the input list, whereby only elements for which the code block evaluates true are returned in the output list, assigned to @data.