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Walter Jessen
I have MySQL and Oracle databases I want to mine for associations between parameters. What's best: Python, Ruby, Perl?? #bioinformatics
Any one of them? Or, whichever language you know best? (Though compiling cx_Oracle might be a bit hairy on OS X) - Rajarshi Guha
I'm new to all three when it comes to trolling through a database. Pros/cons to one over another? - Walter Jessen
Great explanation - thanks Neil. - Walter Jessen
As Neil suggested, Ruby / Python will probably be easier because of all the new ORM stuff. The also tend to be a bit nicer syntactically ;p A word of warning: If using Ruby, you're best to get the 32-bit version of MySQL. The gem is only 32-bit & won't work with the 64-bit (unless they've changed things recently). there's also some flags you need to pass (google will help here). - Mark Bate
If you're using Perl, you can avoid using raw SQL by using DBIx::Class to create an ORM. See the DBIx::Class manual: http://search.cpan.org/~ash.... - Tom Walsh
Why all the Perl bashing? DBIx::Class is awesome. I'm not very familiar with the database stuff in Ruby or Python, but I don't suppose there's a massive difference between the three. What are you doing with the data once you get it out of the database? If you're doing stats, plots etc. then R has RS-DBI. No ORM though, so it might be a faff if the DB schema is complicated. - Cass Johnston
An R-ORM package has just been released: http://www.johnmyleswhite.com/noteboo.... - Tom Walsh
Thanks Tom! - Cass Johnston
@Cass: should we tell them about Moose once they've recovered from the 'Perl does ORM' shocker? - Tom Walsh
Must admit there are things about Perl that annoy me enough to consider switching now and then, but inertia keeps me using it. Not sure CPAN is such a huge advantage anymore. - Tom Walsh
Mark: That's certainly the impression I have from the outside. It is not concerns about lack of libraries that stop me moving from Perl to Ruby/Python; it's just not an issue anymore. They would very definitely stop me moving to Perl 6 when it comes out. - Tom Walsh
Mark: A pity, as Perl 6 is looking very good indeed. If the libs (by that I mean things like DBIx::Class and Catalyst, not the core libs) were there in Perl 6 then Ruby would look much less attractive. - Tom Walsh
Jython or JRuby allow you use Oracle's (pure Java) JDBC driver, which might be less painful to set up. - Eric Jain