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==How to learn== | ==How to learn== | ||
===Get Python=== | ===Get Python=== | ||
| − | Apple computers come with a version of Python installed. It is useful, however, to download a Python package from the official [www.python.org Python website] and install it. I have version 2.5.2, but you may want to install 2.6. Version 3.0 is also available. Many programs written with 2.5 or lower, will not work in 3.0 without considerable editing. So, I would stick to 2.6 for the time being. The installer will place in your computer the Python program, an Interative Developer Environment (IDE) called IDLE and plenty of documentation. Launch IDLE and start programming | + | Apple computers come with a version of Python installed. It is useful, however, to download a Python package from the official [www.python.org Python website] and install it. I have version 2.5.2, but you may want to install 2.6. Version 3.0 is also available. Many programs written with 2.5 or lower, will not work in 3.0 without considerable editing. So, I would stick to 2.6 for the time being. The installer will place in your computer the Python program, an Interative Developer Environment (IDE) called IDLE and plenty of documentation. Launch IDLE and start programming or get [[more help on IDLE]]. |
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==Examples of programs== | ==Examples of programs== | ||
Revision as of 08:24, 13 June 2009
Contents |
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.
How to learn
Get Python
Apple computers come with a version of Python installed. It is useful, however, to download a Python package from the official [www.python.org Python website] and install it. I have version 2.5.2, but you may want to install 2.6. Version 3.0 is also available. Many programs written with 2.5 or lower, will not work in 3.0 without considerable editing. So, I would stick to 2.6 for the time being. The installer will place in your computer the Python program, an Interative Developer Environment (IDE) called IDLE and plenty of documentation. Launch IDLE and start programming or get more help on IDLE.