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Scripting is Awesome!!!!

November 8, 2011

I’m really glad I learned Perl. Ok, I’m no expert but I can do what I need to at this point, which is basically parse text files and automate work flows. What I really like is that it is so easy to automate a data analysis workflow and really doesn’t take much extra time to just put it all into a script. Part of me says I should have sat down a while ago and worked on my programming skills but then the last thing I ever want to do when I get new data back sit down and learn perl or python while my data is sitting on my desktop. So I would always just hammer out the analysis in some inefficient way, at which point I would finish and have lost the need to learn to program. Then it is back to the bench until I get new data back. Repeat cycle. Then I figured out I could learn the basics doing tutorials instead of watching a MTV reality TV show before I go to sleep and let me tell you a perl tutorial is much more efficient at producing the sleep response in humans. Anyway, my point to biologists is that writing basic scripts is pretty easy even for computer shy wet lab biologists.

This is a great place to start:
Unix and Perl Primer for Biologists by Keith Bradnam and Ian Korf

Now if there was only a way to ‘script’ my pipets.


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  1. Sounds familiar to my own recent experience. I recently learned Python and regret not learning it earlier, though R has served quite well. Any particular reason you opted for Perl over Python?

  2. ethanomics permalink

    I’ve had a few stabs at R and usually forget about it after getting really annoyed. I chose Perl simply because I had the Unix and Perl Primer for Biologists pdf sitting on my computer’s desktop and I needed something to read while I while my chromatin was shearing in the Covaris – learning perl in 10 min sessions. But I just asked the same question and from what I gather Python is probably the better choice but if you are heavily vested in one, the differences are probably not enough to make the switch. There are a lot of fans of both languages. I’m going to take a stab at Python now and see what works better for me.

    From what I have read: Python a little easier to learn. More structured.
    Perl good at simple parsing tasks. Less structured which gives you freedom but also can make it difficult to read and maintain code.

    Both a good languages good but also can have difficulties with the volume of data associated with next-gen sequencing (something I’ve already experienced).

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