You can stream it and prevent memory hogs on big data. Additionally, install Text::CSV_XS for speed

use Text::CSV_XS "csv";

my %sums; # Column sums. $sum{column} += $value
my @head;
my @pats;

csv (in => "input.csv", out => undef, bom => 1, kh => \@head, on_in =>
+ sub {

    my ($csv, $row) = @_;

    unless (@pats) {
        # Fetch the "patN" column names, in order. This works
        # for single digit "patN" names, as that was your
        # example. Multi-digit names will require a more complex
        # sort, left as an exercise to the reader.
        # XXX @pats = sort { grep m/^pat\d+$/ } @head;
        @pats = sort grep m/^pat\d+$/ => @head; # This line fixed
        }

    for (@{$row}{@pats}) {
        # You are now iterating over every patN value,
        # in order. Perform your transformation
        }

    # Just an example.
    $sums{$_} += $row->{$_} for @pats;
    });
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update: I changed the grep line which I blindly copied from the original code