Import PennCNV

Author: Sam Gardner, Golden Helix, Inc.

This script imports PennCNV input signal intensity files, where each file contains data for a single sample. The files are expected to have real valued data arranged with a row for each marker and columns containing the marker names, chromosomes, positions, and data values (e.g. Log Ratios and B Allele Frequencies). One spreadsheet is generated for each column of values in the input files.


Import PennCNV.py

Download Documentation Documentation

Recommended Directory Location

Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\SVS\Import

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 SVS Import menu.


Need a Custom Script?

Scripts

Need a script and don't feel you have the bioinformatics expertise 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 »

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.

Python Learning Resources