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

SNP Cluster Plots

Author: Greta Linse Peterson, Golden Helix, Inc.

This script creates scatter plots based on A and B allele intensities that can be split on SNP genotypes to create tri-colored cluster plots. The script will work for up to 100 SNPs at a time.

You will need genotypes for up to 100 SNPs, and you must also have the Affymetrix CEL files available for import.

This document provides instructions on how to import the intensity data from the CEL files, how to use the script, and how to split the scatter plots based on genotypes.

	SNP Cluster Plots.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 open SVS and go to Tools >Open Folder > UserScripts Folder. If you save the script to the proper folder, it will be accessible from the project navigator Tools menu.