Python: the powerful Programming Language
Python is a powerful high-level OOP (Oriented Object programming) programming language. I use it for bioinformatic / scientific computing, scripting, parsing and more... You can easily extend the standard library with third party tools or other language ( C, C++, R, Matlab...).
Python courses and tutorials
- Dive Into Python (english)
- Dive Into Python (french - plongez au coeur de python)
- Cours de python by P. Fuchs (french)
- Python Quick Reference Card
Python libraries selection
Here, my personal libraries selection. This is not a comprehensive list of third party tools but a seletion of tools that I often use... and recommend ! For a repository of "all" additional software for Python, please visit the Python Cheese Shop site which contains more than 2,000 packages !
Distribution
| Name | Description | Version | Link |
|---|---|---|---|
| Original Python | The original python... | 2.5.2 |  |
| Active state | Nice 'free' distribution. | 2.5.2.2 | |
| Enthought | An all-in-one nice distribution providing a lot of library (Pil, Numpy, Scipy, ...). | 2.4.3 | |
Documentation tools
Sphinx is a python document generator based on reStructuredText markup language. It can export documentation in HTML Latex or HTML.
Do you like beautiful highlighted code ? If yes, you can easily do that using Pygments, a python syntax highlighter.
Libraries
| Name | Description | Version | Link |
|---|---|---|---|
| Numpy | Basic N-dimensional array manipulation tools (the successor to both Numeric and Numarray). | 1.1.1 | |
| Scipy | Scientific tools for Python (including linear algebra, optimization, integration, special functions (like hamming), signal and image processing, statistics, genetic algorithms...). The core library is numpy. | 0.6.0 | |
| RPy | R python binding, simple and robust interface to the R programming language. | 2.0.0a2 | |
| PyML | Machine learning framework (SVM, nearest neighbor classifiers). | 0.7 | |
| Biopython | Library for computational biology. I don't like the biopython fasta parser. I use "fasta" (see below) which have a more pythonic code (iterator). | 1.47 | |
| CoreBio | Library for computational biology with "essential" tools: sequences IO, alphabetic sequences, fast and clean. | 0.5.0 | |
| Fasta | Simple but efficient fasta parser by Thomas Mailund. | 1.0 | |
| NetworkX | Python graph library (the successor to pygraphlib). | 0.36 | |
| pyNetConv | Convert some network file formats (.net .sif cytoscape .gml). | 0.12 | |
| PyYAML | Yaml network format parser. | 3.05 | |
| Matplotlib | 2D plotting library. | 0.98.3 | |
| PIL | Python Imaging Library | 1.1.6 | |
| Pyx | Python package for the creation of postscript and pdf documents. | 0.10 | |