A framework for proteomics data analysis.
Project description
What is Pyteomics?
Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis, such as:
calculation of basic physico-chemical properties of polypeptides:
mass and isotopic distribution
charge and pI
chromatographic retention time
access to common proteomics data:
MS or LC-MS data
FASTA databases
search engines output
easy manipulation of sequences of modified peptides and proteins
The goal of the Pyteomics project is to provide a versatile, reliable and well-documented set of open tools for the wide proteomics community. One of the project’s key features is Python itself, a open source language increasingly popular in scientific programming. The main applications of the library are reproducible statistical data analysis and rapid software prototyping.
- Pyteomics is hosted at the following sites:
Python package @ Python Package Index: http://pypi.python.org/pypi/pyteomics
project documentation @ python.org: http://packages.python.org/pyteomics
source code @ bitbucket: http://hg.theorchromo.ru/pyteomics
mailing list @ Google: https://groups.google.com/group/pyteomics
Project dependencies
Pyteomics uses the following python packages:
matplotlib (used by pyteomics.pylab_aux)
lxml (used by pyteomics.mzml, pyteomics.pepxml)
GNU/Linux
The preferred way to obtain pyteomics.biolccc is via pip Python package manager. The shell code for a freshly installed Ubuntu system:
sudo apt-get install python-setuptools python-dev build-essential sudo easy_install pip sudo pip install lxml numpy matplotlib pyteomics
Windows
Download pre-compiled binary packages for Pyteomics dependencies:
Download a pre-compiled binary Pyteomics package from the list below.
OR
If you have Enthought Python Distribution / ActivePython, execute in the command line:
easy_install pip pip install lxml numpy matplotlib pyteomics
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