Wednesday, October 5, 2011

Perl vs. Python dog fighting

So Python is the hot new thing and I, as an old Perl dog, should make a statement on the subject.  You're guessing I'm going to tell you why Perl is better?  You guessed right!  Specifically, I want to address the arguments that Python encourages better programming practices or that it is better for teaching.  This is true.  However, as educators (in the field of bioinformatics but also elsewhere) we need to consider what is our ultimate goal - easy training process or the product of skilled trained people.  The analogy that immediately comes to mind is naturally fighter training in the Israel Air Force.  In the first decades of Israeli history, when the threat of annihilation was imminent and the culture was very much influenced by the Soviet model, Israeli fighter pilots were taking lots of "stupid" risks during training for combat.  As a result, some classes had lost even 50% of the fighter pilots over their 20 years of service, and training accident were more common than KIAs.  The other result was that Israeli pilots could win fights against less well trained pilots even when heavily outnumbered.  This practice have been reversed in the more recent decades (after stabilization of the state and influence of American culture...) and now training accidents are much less common.  We cannot judge if Israeli pilots are not good dogfighters any more because (a) the last heavy air-to-air fighting was in 1982 and (b) dogfighting is less important with modern fighter jets.

Nevertheless, the point remains and the analogy is useful.  Perl requires harder training but will ultimately be more powerful.  Python is nicer for teaching but more limited.  Python is a more constrained language with more proper syntax and object oriented design, which are attractive qualities for the teaching of programming.  Perl is the "Pathologically Eclectic Rubbish Lister" (Larry Wall).  It doesn't restrict the programmer from using bad programming practices.  And it is true that you can find a lot of badly written Perl code out there.  But this is not because Perl is a bad language.  It is because some Perl programmers are lacking good education in programming.  Guns don't kill people.  People kill people.  A well written program can be written in any language if the programmer knows how to structure the code intelligently and use syntax choices that make clear and understandable code (rather the notorious possibility for code obfuscation in Perl).  So it is up to us as educators to produce students well educated in good coding practices.

The flip side of this coin is that Perl is much more versatile, flexible, and powerful than Python (and other alternatives).  It allows more efficient development of new code, i.e., shortening the time and effort from the moment you sit down to write a bit of code to the moment you can run it and get your results.  This is highly desirable for practical programming such as short scripting for bioinformatic analysis.  So as educators of practical programmers we should make the effort to teach good programming practices while using the most powerful language available for our students.  At the present time, especially for bioinformatics, this language is Perl.  Teaching constrained languages to "force" our students into good practices is taking the easy way out as educators and handicapping the future potential of the people we train.

Monday, September 12, 2011


This is a very exciting day - today the MAFFT sequence alignment web server added a button to its results page that redirects users to the GUIDANCE web server.  This will encourage the many MAFFT users to test the robustness of their alignments using GUIDANCE.  I'm hoping we'll get a substantial exposure through MAFFT and increase the awareness to alignment confidence measures and to our GUIDANCE server.

This was made possible by a collaboration with Prof. Kazutaka Katoh from Kyushu University who developed MAFFT.  He generously devoted his time to coordinate the integration of the two servers.  On the Tel Aviv side the credit goes to Haim Ashkenazy who developed the GUIDANCE web server.