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use Math::Pari qw/ PARI /;
sub PARIdo {
...
    $s =~ s/[{}\s]+//g;
    PARI($s);
}

PARIdo(q{
  mygcd(a, b) = {
...
  }
});
print PARI("mygcd(12,8)");

my $v1 = PARI(12);
my $v2 = PARI(8);
print PARI(qq{mygcd($v1,$v2)});