ISCNSNAKE 2.0

A parser for ISCN data.

ISCNSNAKE : ISCN Structural and Numerical Analysis of Karyotype Entries

ISCNSNAKE is a tool to use with ISCN : the International System for Cytogenic Nomenclature written in python 3.7. The repository contains three python files, one is the core of the module (ISCNParser.py) and the second (run_SNAKE.py) is a quick script that executes the main function of ISCNParser. Most features are accessible through the console menu that opens when the script is ran but if you want to automate multiple files or do something more complicated it is suggested that you import the module into your own script. The third script (quick_run_SNAKE.py) runs ISCNParser at the default settings with users only having to specify the location of the Mitelman database on their computer, the desired output folder and filenames, and any criteria they wish to use as filters. For a description on how to use these filters consult readthedocs.org/ISCNSNAKE/

SYSTEM REQUIREMENTS

Python 3.6 or greater

Python modules

• pandas
• numpy

INSTALLATION

1. Open either terminal or command line in the fold you place the download (this folder).
2. Input " python setup.py install --user "
3. You should be able to run the program from anywhere with the upcoming instructions.

TUTORIAL

Authors

• Connor Denomy ([e-mail]) - Lead author

Acknowledgments

• Samuel Germain for creating the prototype of this program in shell/perl and providing the basis for the core algorithm
• cyDAS(cyDAS.org) for helping to check proper function. Unfortunately became abandonware late 2018.
• Bjorn Haave for assisting
• Vizeacoumar lab