What is Python?

Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. Integrating Python into SVS 7 provides full programmatic access to many of the software's features enabling the augmentation of existing tools, creating entirely new ones, automation of work flows, integration with other programs and more.

Python Learning Resources

» SVS 7 Scripting Reference
» Python.org
» Beginners Guide to Python

Affymetrix B Allele Frequency Calculation

Author: Greta Peterson, Golden Helix, Inc.

Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker.

For information on accessing B Allele Frequencies for Illumina data, see www.goldenhelix.com/Downloads/SVS/ExportingDSF-GenomeStudio_v4.doc

	Affymetrix B Allele Frequency Calculation.py
	Documentation

Recommended Directory Location

Need a Custom Script?

Need a script and don't feel you have the bioinformatics exptertise to write it yourself? Click the link below to request a custom script and we'll see what we can do to help.

» Request Custom Script

Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\SVS\Tools

Note: The Application Data folder is a hidden folder on Windows operating systems and its location varies between XP and Vista. The easiest way to locate this directory on your computer is to click on the AppData shortcut in your C:\Program Files\Golden Helix SVS\ directory. If saved to the proper folder, this script will be accessible from the project navigator Tools menu.