Beginner to BioPython - (Sep/05/2006 )

Hi everyone,

I've been reading a nice O'Reilly Python book for the past 2 weeks. I have acquired a wealth of knowledge thus far and plan to delve into the BioPython module for Python (in the near future).

This might be a silly question, but none of my professors work with Python, so I came to this forum in search of possible answers. I am just curious to know: How competent in Python, and how long should I spend with it before I move on to BioPython?


I would be highly appreciative to responses.
Thank you,

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Hello.

Python is a great language (although I prefer perl). The great thing about python is that it is, as you are probably aware, object orientated (OO). The OO design makes the code clean and the use of white space (although irritating at times) makes python very easy to read. Like bioperl and biojava, biopython is not a single module but a collection of modules which you can plug into your own code to achieve specific results, such as removing sequneces from a remotre database or parsing psi-blast output. I must admit that I am yet to use biopython (although at the start of next month I will be making some use of it). Going from the bioperl experience that I have, I hope that the python setup is better than the perl one... as for how long you should use python before trying biopython, it depends upon how comfortable you feel with python.... I would suggest you sign up to the beginners python list as they are a fantastic bunch and are alway happy to help (some are even biologists)

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Hi perlmunky,

Thanks for your reply. I will surely keep upto date with my Python programming.

Out of curiosity though: How long did you learn perl before you began writing bioinformatics scripts? Did you buy Perl books and teach yourself? Did you attend classes?

Thanks

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ah, I started writing VB and HMTML when I was a secondary school (self taught). When I started my undergraduate degree I started learning Python (not for biological stuff but for naughty reasons !). I then did a masters degree in bioinformatics learning Java (basic) and perl. I was taught perl by a Dr S Andrews (serious perl head) at Babraham Institute. Before I started my PhD I learnt C++. Before I started coding perl I only had two weeks worth of experience with perl however I was not new to programming.

If you want to teach yourself then I suggest you get copies of Learning Perl by Schwartz & Phoenix and Programming Perl by Wall, Christiansen & Orwant. I strongly recommend against you using either of the James Tisdall books (perl for bioinformatics and mastering perl for bioinformatics)...

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