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

Export MACH PED_DAT Files

Author: Greta Peterson, Golden Helix, Inc.

This script exports MACH/Merlin PED and DAT formatted files. Run this script from a pedigree spreadsheet that can contain as many phenotypes as desired.

The user will be provided with the option to create one file per chromosome if a marker map is applied to the pedigree spreadsheet. This option is recommended as MACH can crash if run on a dataset with too many markers.

Note: This script assumes that genetic data contains only allele encodings accepted by MACH (1, 2, 3, 4, A, G, C, T). Also, for AGCT encoded genotypes, it is assumed that the genotypic data is represented by the same strand.

	Export MACH PED_DAT Files.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\File

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 File menu.