Convert Dosages to Genotypes
Author: Autumn Laughbaum, GHI
This script converts allelic dosage values to genotypes based on user-specified thresholds. The dosage data may be in Single- or Double-Dosage format and may have samples in the row labels or column headers. If the samples are in the column headers, the spreadsheet may contain map information and allele translation values.
Convert Dosages to Genotypes.py
Recommended Directory Location
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 many operating systems and its location varies between operating systems. 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.
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What is Python?
Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. Integrating Python into SVS 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.