Bioperl: relative-majority consensus, fast code sought

[Matthew Pocock]

I doubt that it will be faster as perl has to do extra work to remove the
letters matched, find memory to put the new string in, and free the old string.
Also, I think that tr/// has some gotcha's when the pattern is a variable
string. In general, avoid making perl alocate/re-alocate memory. That means
don't modify things unless you want the modified result.
Also, remember that by default Perl doesn't return memory to the system untill
it exits. It can be internaly re-used by perl for new objects/primatives, but
is not available to other processes.

Matthew
Gustavo Glusman wrote:

> Shouldn't this be faster?
>
> $_ = $string;
> foreach $letter (qw/A T C G/) { $count{$letter} = tr/$letter//; }
>
> The idea being that the string studied gets shorter every time. Added bonus
> is being left with the non-ACGT letters in $_ at the end.
>
>      ____________________________________________________________
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