Optimal Scripting Language Config For Bioinfomatics In Windows 7

Question

[Occam]

coming from a statistical genomics background in which i used R + plink + stata for almost everything. now doing more computationally intensive bioinformatics and finding it arduous to code in R. have begun to learn perl and python. wondering what config you would recommend for bioninformatics work in windows environment. currently mostly writing perl in notepad++, but have not invested that much time, so now would be good time to switch.

basically wondering what text editor/IDE + scripting language (either perl or python) combo you would recommend for windows. pls no "use unix/linux" cmts. thx!

Answer 1

[Niek De Klein]

I would say for python use eclipse with pydev. It's a very nice open source IDE, definetly my favorite one for python I've used so far. I'm sure there is a plugin for Perl too, but since I haven't used any Perl IDE's I'm not going to advice you on that. [?] In my personal opinion I would advice you to start learning python. It is a lot easier to read and understand than Perl. However, their functionality is very similar so what you can do with one you can do with the other, so I would say use the one you feel most comfortable with. But since you only just started I would say switching is the right choice. [?]Python does have a very nice library to use R in python, rpy2. But I'm sure you can find one for Perl too. [?]

I would also advice you to read my question about when to choose python above perl, there are some very good answers there.

[Davy]

Eclipse does indeed have plugins for Perl. They pretty good, but I would not AS good as PyDev. That might just be because I prefer python though. Eclipse also has a plugin for R (statEt) although I use Rstudio and the Revolution R.

Answer 2

[Zev.Kronenberg]

Perl has great libs for bioinformatics including bioperl and gmod. As for an editor I would use emacs. It supports so many languages like R and Perl. You can run scripts directly from emacs. It also works on Windows 7.

Sorry for saying this, since you asked us not to:

Consider a linux dual boot? Many great tools will not work in the windows environment.

Answer 3

[Damian Kao]

I personally prefer python to perl. Perl has more resources and established libraries. Python is more agile. There are plenty of questions on biostar that lists the pros/cons of the scripting language you choose.

For a text editor, I like [?]sublime text 2[?]

I know you don't want to hear it and I've encountered plenty of people who are adamant about using windows. But you are really doing yourself a disservice by not using linux/unix.