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

Activate ATCG SNPs to Flip Strand

Author: Joost W. Morsink and Sander W. van der Laan, University Medical Center Utrecht

This script can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data. First the script will identify all A/T, T/A, C/G and G/C SNPs where the minor allele in your dataset differs from the minor allele in the reference dataset. Then it will further identify which of those SNPs have a minor allele frequency less than a user-specified value in your dataset. These SNPs will be activated and an active subset will be created. The subset can be used to flip strands before analysis.

	Activate ATCG SNPs to flip strand.py
	Documentation

Activate ATCG SNPs to Exclude SNPs

This script can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data.  First the script will identify all A/T, T/A, C/G and G/C SNPs where the minor allele in your dataset differs from the minor allele in the reference dataset. Then it will further identify which of those SNPs have a minor allele frequency greater than or equal to 0.40 in your dataset. These SNPs will be activated and an active subset will be created. The subset can be used to exclude the SNPs from the analysis, which had strand orientation that was hard to determine.

	Activate ATCG SNPs to exclude SNPs.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\Quality Assurance

Note: 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 Quality Assurance menu.