[Purdue-pm] RADpools

[Phillip San Miguel]

On 10/20/2010 8:59 AM, Rick Westerman wrote:
>
>> The code in question (with extra comments):
>>
>>     for my $i ( 1 .. $mid_length ) {
>>         for my $base (qw{A C G T}) {
>>             my $fuzzycode  = $mid;
>>             my $prebase_i  = $i - 1;
>>             my $postbase_i = $mid_length - $i;
>>             $fuzzycode =~ s{
>>              ^([ACGT]{$prebase_i})     #capture bases, if any, before
>>     current base
>>               ([ACGT])                 #current base
>>               ([ACGT]{$postbase_i})$}  #capture bases, if any, after
>>     current base
>>             {$1$base$3}xms;            #replace current base with $base
>>             push @{ $mid_pools{$fuzzycode} }, $pool_name;
>>         }
>>     }
>>
>> Actually, I don't see any problem with this code.
>
> Readability is the issue.   IMHO, the author is using a sledgehammer 
> when a peen hammer would do.  Speedups are not the issue.  The 
> following is much more clear ... especially to the the novice Perl 
> programmer who is not that familiar with regexes.
>
>
> for my $i ( 0 .. $mid_length - 1) {
>     for my $base (qw{A C G T}) {
>         my $fuzzycode = $mid;
>         substr($fuzzycode, $i, 1, $base);
>         push @{ $mid_pools{$fuzzycode} }, $pool_name;
>         print "$fuzzycode\n";
>     }
> }
>
>
> Explaining substr should be a piece of cake compared to regex captures 
> and replacements.
>
Your code is more compact. But the original code spoke to me. I could 
immediately tell what the author intended to do. Your more compact 
implementation does something very similar to what the original code 
does, but were I to read it de novo, I doubt I would have any idea what 
it was doing.

Regex captures and replacements are important parts of perl. So they 
need to be explained sometime. I think you guys are hitting the "I saw a 
problem and decided to use a regex to solve it, now I have two problems" 
meme too hard. Unfortunately the meme is funny, which gives it more 
persistence than it should be allocated.

That said, now that I do understand the code, I would go with the more 
compact form.

Phillip
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