From: Martin Hansen <mail@...>
Date: 2010-08-30T23:55:54+09:00
Subject: Re: Speed issues iterating over chars

> You could do this though
> 
> seq.gsub! /./ do |m|
>   scores[$`.length].ord - BASE_SOLEXA < cutoff ? m.downcase! : m
> end
> 
> Not too nice though.  You could however do some preparation, e.g.
> store scores as an Array of Fixnum instead of using #ord.

Yes, converting scores to arrays is bad since the scores are parsed from 
files as strings (millions of them). And I am unsure if substr 
substitutions are very efficient ...

We need to trick this into the regex engine somehow.

How about transforming scores to a mask string like this: 000111 where 1 
indicates that the corresponding sequence char should be lowercased 
(that can be done with tr). Then we plug this onto the sequence string:

seq = "ATCGAT000111"

And then we construct a regex with a forward looking identifier that 
reads the mask and manipulates the ATCG chars?


Martin


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