I wish I had… started with python earlier…

So far, my bioinformatics work has used a melange of perl, R, and bash scripting. While this has worked pretty well, it does have limits. For one, it is very not portable (bash scripting). I’ve already had problems with distributing software.

I wanted something that I could distribute in an easier way, yet had the advantages of perl. I found Jython, which is Python-in-Java. For me, the big deal is not use of Java libraries, but rather that the language would compile to Java byte-code and hence would be easy to distribute.

But I found that Python is much more than this: the interactive environment, for one, makes me ok with not having my unix/linux toolbox when I am stuck on the windows side.

And Python has a lot of nice features for bioinformatics work, including convenient types like sets (as of version 2.4) and even comes with sqlite (which I have not used from python, but want to)…

Anyways, for now, I am a fan.

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One Response

  1. Great to see a new bioinformatics blog on the block.

    Like you, I’ve been a Perl/R/shell man for some years, am tiring of it and intrigued by the possibilities of Python (and perhaps, Ruby). Looking forward to reading your posts.

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