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

Alternate Allele Frequency

Author: Mike Thiesen, Golden Helix

This script calculates the percentage of alternate alleles over all samples for each variant. The spreadsheet is expected to have samples as rows and a marker map applied to its columns. The marker map must contain a reference base field.

The resulting spreadsheet has variants as rows and the marker map applied rowwise. The spreadsheet has columns containing the reference count, alternate allele, alternate allele frequency, reference allele count and alternate allele count. Optionally, an annotation probe track (IDF) can be created.

	Alternate Allele Frequency.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\Spreadsheet\Analysis

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 saved to the proper folder, this script will be accessible from the spreadsheet Scripts menu.