[Purdue-pm] RADpools

[Rick Westerman]

> 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.

-- 
Rick Westerman westerman at purdue.edu Bioinformatics specialist at the 
Genomics Facility. Phone: (765) 494-0505 FAX: (765) 496-7255 Department 
of Horticulture and Landscape Architecture 625 Agriculture Mall Drive 
West Lafayette, IN 47907-2010 Physically located in room S049, WSLR 
building
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