First, use Text::CSV_XS instead of Text::ParseWords - it reads more like the spec that way (having your code match your spec is always good in my books). Second, I don't see any commas in your original data, so there is an obvious mismatch.

Next, you are hardcoding your week number in your code. Don't do that. Accumulate it in a hash. I would even go so far as use a hash of hashes with separate fields for the sum and count.

Also, learn to use proper indentation. Your code is quite simply a mess. It's very difficult to follow nesting, and would get impossible to follow fairly quickly.

I also see a while inside a while, both reading from the same file. That's nonsensical. Instead, just read and discard a single line: scalar <$fh> should do it.

my %data;
my $csv = Text::CSV_XS->new();
scalar <$fh>;
while (my $row = $csv->getline($fh))
{
  $data{$row->[0]}{sum} += $row->[1];
  $data{$row->[0]}{count}++;
}

for my $weeknum (sort keys %data)
{
  printf "%s %d %.1f\n", $weeknum,
                         $data{$weeknum}{sum} / $data{$weeknum}{count}
+,
                         $data{$weeknum}{count};
}
[download]

That should give you enough to go on.

Update: s/comments/comma/ in the first paragraph