What have you tried already? See How do I post a question effectively?, but you have at least provided some good sample input and output, so that's a good start.

See Text::CSV for the CSV processing.

use Text::CSV 'csv';

my $aoh = csv ( in => 'input.csv', headers => 'auto' );

# 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.
my @pats = sort grep /^pat\d+$/, keys %{$aoh->[0]};

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

for my $row ($@aoa) {
    for (map { $row->{$_} } @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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This is just a skeleton to get you started. Certainly more code than you posted. The code will require modification, does not output anything, and some of my simple logic may prove to be inadequate, but hopefully illustrates the general approach you might take. Definitely read the Text::CSV manual thoroughly, and probably perldata as well.