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grep { @input_B eq $_ } @input_array

for my $inputKey (@input_array)
{
    if (grep { $inputKey eq $_ } @input_A) ...
}

use strict;
use warnings;
...
    print "CC0[$key] = $CC0\n";
    print "CC1[$key] = $CC1\n";
}

16:27 >perl 1992_SoPW.pl
N1: only 1 input is PI
...
CC1[N3] = 1

16:27 >

$primaryCC0{$inputKey} = [1, 1];