Being most familiar with Java and Ruby, Python seems a little in between, but one feature that stuck out was the regular expression syntax.  Python let’s you put a ‘r’ in front of the quote to denote raw input.  This means you don’t have to escape back slashes twice (ala Java).

For those not familiar with regular expressions, here is an example of a regular expression in a few languages:

Java:
Find Slashes: "[\\\\/]"

Python:
Find Slashes: r"[\\/]"

Ruby:
Find Slashes: /[\\\/]/

This is just a simple example to illustrate a point, but look at Java.  Find slashes has 4 backslashes.  Even if regular expressions were typically this simple (they’re not), that seems unnecessary.  Anytime it’s necessary for a backslash to make it to the regular expression processor, there much be two in the regular expression.  Another quick example, to find a period (.) the regular expression would be “\\.”.  This compounds very quickly, and makes it painful to use regular expressions in Java.

I can’t understand why Java wouldn’t adopt the python syntax of putting a ‘r’ in from of a string to denote raw input.  At quick glance, it doesn’t seem as though it would break any currently in use regular expressions because the old syntax would continue working as expected.  It’d make them better for the future.

Here are some Regular Expression resources that I find useful:

http://www.rubular.com/ A Ruby Regular Expression Tester

http://www.fileformat.info/tool/regex.htm A Java Regular Expression Tester

I’ve since updated 3 of the benchmarks; I sped up reverse-compliment to be 2x faster than the previous. I’m not a Ruby expert by any means, but I was able to get a speedup. I don’t know if the other languages are in the same state, but they may be…

Anyway, the Fasta benchmark is the one that I most recently updated. It took me a while to get a decent speedup. It turned out the Array#find is slower than Array#each with a break statement. Making this switch is what got the biggest speedup out of the program.

I wrote a benchmark showing the difference in runtime:

require 'benchmark'
 
N = 300
table = (0..300).to_a
Benchmark.bmbm(8) do |x|
  x.report("Array.find") {
    N.times do
      table.each do |find_num|
	table.find do |num|
	  num > find_num
	end
      end
    end
  }
 
  x.report("Array.each") {
    N.times do
      table.each do |find_num|
	output = nil
	table.each do |num|
	  if num > find_num then
	    output = num
	    break
	  end
	end
      end
    end
  }
end

The results:

Ruby 1.8.6       user     system      total        real
Array.find  12.120000   0.020000  12.140000 ( 14.647705)
Array.each   8.150000   0.030000   8.180000 (  9.734463)

JRuby 1.1.4      user     system      total        real
Array.find   6.738000   0.000000   6.738000 (  6.738407)
Array.each   5.365000   0.000000   5.365000 (  5.364320)

Now, I’m running this on an admittedly dated machine. Again, I’m nowhere near a ruby expert, so if someone sees a way to make the benchmark more fair let me know, and I’ll update it. I can’t say anything about how this would run in YARV when that is released.

Here is a link to the Ruby Fasta benchmark on the Language Shootout:

Ruby Shootout: Fasta