I understand that each programming language has its advantages and disadvantages. Had some experience on python and perl. I start reading about ruby, bioruby and different questions come to my mind. Away from personal prefereces, regarding syntax for example, what should guide the choice for python, perl, ruby or other languages? There are true advantages of one language instead of other?
While it has been covered several times, and ultimately comes down mostly to personal preferences, I think these are worth having from time to time as people update (and languages too). I've become a python convert. I learned programming initially in C and later added Java and Perl. When I started grad school I was coding pretty much exclusively in Perl with one project that I inherited in Python as there was existing legacy code. I stuck mostly with Perl throughout my PhD but started using Python more often. After starting my post-doc I decided to try doing much of my work in Python instead of Perl and absolutely fell in love with it for genomics.
Perl is still superior for arbitrary text parsing. I find it much less cumbersome when it comes to regular expressions for instance. But Python has so many great libraries for handling delimited-file types, defaultdict is powerful, and it has lots of great genomics libraries that are truly object oriented compared to Perl.
Basically between PyVCF, PyBedTools, the csv package, defaultdict, and IntervalTree I can do some really powerful analyses with Python in a really efficient manner compared to Perl.
One comparison of perl python and ruby
And a paper "A comparison of common programming languages used in bioinformatics" Mathieu Fourment* and Michael R Gillings
And a comparison regarding "mainly: loops, dynamic arrays with numbers, basic math operations."
This comparison, on doing a typical bioinformatics task (calculating GC content) in a bunch of different languages, might give you some pointers: http://saml.rilspace.org/moar-languagez-gc-content-in-python-d-fpc-c-and-c
If you click the language names in the list under the graphs, you can see code examples, to get an idea of code readability.
As you can see, python, by using PyPy, does a very good job and is comparable to compiled languages. If you want slightly better performance still, while wanting to keep code compact and readable, D would be my next bet. (Compare code: Python, and D).
Found an interesting post