Genome Segments Readme

What does it do ?

This program uses input data about segments and functions on the genome to compute: overlap between segments, the correlation between functions or the average of a function on certain segments.

Where to put data ?

The default location for data is in "../data/". You can also use a folder of your choice and specify it when you run the program.

How to run it ?

This is a python program and can be run from the command line (for example in bash or another shell) using:

  python main.py

You will then be asked to enter the file path to the data, and select the data files that you wish to use.

Dependencies

numpy

Implementation choices

The current implementation uses methods from the numpy packages for the Pearson correlation coefficient and file reading because these are highly efficient. Therefore numpy needs to be installed.