grep { @input_B eq $_ } @input_array

##</code><code>##

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

##</code><code>##

use strict;
use warnings;
use List::Util qw( any );

my @input_array = qw( N1 N2 N3  N6  N7      );
my @input_A     = qw( N1 N3 N11 N11 N10 N16 );
my @input_B     = qw( N3 N6 N2  N7  N16 N19 );
my %primaryCC0;

for my $inputKey (@input_array)
{
    if (any { $_ eq $inputKey } @input_A)
    {
        if (any { $_ eq $inputKey } @input_B)
        {
            @{ $primaryCC0{$inputKey} } = (1, 1);
        }
        else
        {
            print "$inputKey: only 1 input is PI\n";
        }
    }
    else
    {
        print "$inputKey: this is a wire\n";
    }
}

for my $key (sort keys %primaryCC0)
{
    my ($CC0, $CC1)  = @{ $primaryCC0{$key} };
    print "CC0[$key] = $CC0\n";
    print "CC1[$key] = $CC1\n";
}

##</code><code>##

16:27 >perl 1992_SoPW.pl
N1: only 1 input is PI
N2: this is a wire
N6: this is a wire
N7: this is a wire
CC0[N3] = 1
CC1[N3] = 1

16:27 >

##</code><code>##

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