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Learning Python

This page is an invitation to learn Python and apply it to bioinformatics. It uses my limited experience in this area to demonstrate that even if you never were exposed to any programming it is possible to learn enough Python to write programs that analyze sequence data and produce results. In addition, programming is fun and it beats Sudoku and crossword puzzles as a constructive brain teaser and past time. --Luca Comai

How I learned

I first tried Perl, another programming language, and became frustrated by my inability to understand the syntax. Now, I am not clear why this is the case because Perl is really not difficult. This just goes to show that learning programming may seem difficult. I dropped the effort. A few months later, I decided to try again. Victor Missirian, a bioinformatician who works with me, showed me the Python tutorial written by the Python inventor, Guido von Rossum. It was very simple and so I decided to try again. I downloaded the Python package from python.org, bought a couple of books and never looked back. I started writing a program that would inventory and report all the restriction fragments in a genome. Having a specific objective helped me focusing and motivating me. Since then I have written dozens of little programs to do all kinds of stuff, such as parsing Illumina sequencing files, grading my class, performing in silico comparative genomic hybridization and so on. Now, do not get me wrong, I am really a beginner and there is a lot that I do not know and will most likely never learn. But this is really the good news. You do not need a degree in computer sciences to have fun and be productive.

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