From: Robert Klemme <shortcutter@...>
Date: 2010-08-30T18:02:11+09:00
Subject: Re: Speed issues iterating over chars

2010/8/30 Martin Hansen <mail@maasha.dk>:
> Hello all,
>
>
> This snip of code needs more speed. Ideas? What is the state of Ruby and
> Inline C?
>
>
> Cheers,
>
> Martin
>
>
>
> class Hash
>  BASE_SOLEXA = 64
>
>  # Soft masks sequence residues where the corresponding quality score
>  # is below a given cutoff.
>  def mask!(cutoff)
>    if self.has_key? :SEQ and self.has_key? :SCORES
>      seq    = self[:SEQ]
>      scores = self[:SCORES]
>      i      = 0
>
>      scores.each_char do |score|
>        seq[i] = seq[i].downcase if score.ord - BASE_SOLEXA <= cutoff
>        i += 1
>      end
>
>      self[:SEQ] = seq
>    end
>
>    self
>  end
> end

What about using String#gsub!?

# untested
seq.gsub! /(?:#{(0..(BASE_SOLEXA+cutoff)).map{|ch|"\\u00%02x" %
ch}.join("|")})+/ do |m|
  m.downcase!
end

You could speed up calculation of the regexp by placing this in the
default block of a Hash, e.g.

RXS = Hash.new {|h,cutoff| h[cutoff] =
/(?:#{(0..(BASE_SOLEXA+cutoff)).map{|ch|"\\u00%02x" %
ch}.join("|")})+/

and then

seq.gsub! RXS[cutoff] do |m|
  m.downcase!
end

Kind regards

robert

-- 
remember.guy do |as, often| as.you_can - without end
http://blog.rubybestpractices.com/