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

Convert Binary and Integer Values to Genotypes

Author: Greta Linse Peterson

This script recodes binary and integer genotypes to the standard genotype format of A_A, A_B, and B_B. Prompts for value of A_A, A_B, and B_B. All other numbers are encoded as missing. Thus if there is multi-allelic data in the spreadsheet, all numbers other than those specified will be encoded as "?".

*Note: Assumes that the spreadsheet will only consist of binary and integer columns to recode, all other column types will be added to the new spreadsheet as is.

If a marker map was applied to the original spreadsheet it is reapplied to the new spreadsheet.

	Convert Binary and Integer Values to Genotypes.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\Edit

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 Edit menu.