From Comaiwiki

(Learning Python)
(How I learned)
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==How I learned==
 
==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.
 
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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==How to learn==
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===Get Python===
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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. [[idle This page]] gives more details on how to use IDLE.
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==Examples of programs==

Revision as of 08:22, 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. idle This page gives more details on how to use IDLE.

Examples of programs

Personal tools