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

Create Table for Significant Regions

Author: Ingo Helbig, UK-SH Kiel, ingo.helbig@epilepsygenetics.com

Creates a spreadsheet with significant regions from a spreadsheet of p-values (in the first column). The input spreadsheet has to be marker-mapped.

This script extracts p-values more extreme than a certain significance value (cutoff) and combines the remaining markers into segments. If two markers are on different chromosomes or more than a certain distance apart (split), a new region is created.

Standard values for cutoff: 0.0001
Standard values for split: 500,000 bp (500 kb)

	Create Table for Significant Regions.py
	Documentation

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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.

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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 Analysis menu.