Name: gtr-tools
Owner: NMDP/Be The Match Bioinformatics Research
Description: null
Created: 2015-08-03 15:53:10.0
Updated: 2015-08-10 17:20:04.0
Pushed: 2015-08-10 17:20:04.0
Homepage: null
Size: 441
Language: Python
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A set of Python scripts to work with data in the NIH Genetic Testing Registry (GTR).
These programs all run in Python 2.7.
Recommended:
To skip all the steps below, I suggest installing Continuum's Anaconda, which I highly recommend for scientific computing. It already includes all the modules needed to run these scripts, and many others which makes installation of frequently used non-built-in modules easier, it does not affect other python installations on your machine, and the conda package manager is a great way to handle virtual environments.
Traditional, cumbersome way:
pip install -r requirements.txt*Note: The above steps may require even extra effort to get installed onto osx/linux. lxml may require more dependencies to be installed which can be difficult. Also, tkinter is not in the requirements.txt since it is a built-in but certain versions of OSX/Linux and their shipped Python version do not include it which will require manually installing as well. I suggest just installing Anaconda from the start to avoid complications.
Search provides a GUI program for searching GTR and downloading data. It utilizes the E-utilities.
NGS is a hot topic in bioinformatics and genetic testing. These scripts provide some insight into the growth of NGS in the GTR and best practices for that data.