Go-Processing

My solution for Holm Group's coding test (summer 2019).

Regarding the assignment

The requested code is located in two files:

• go_processing.py
• go_processing_functions.py

The requested output can be found in

• example_data/top50_most_common_go_classes.tsv

The rest is just for fun 😄

Applying the code

Prerequisites

Requires only Python3 to run

Setup

To use go-processing, you can

git clone https://github.com/otsovelhonoja/go-processing

or just download go_processing.py and go_processing_functions.py to your desired folder.

This repository also contains the sample data for which this program was initially built for. These files are located in compressed format in the data/ folder. For simplicity's sake, it's best to download this folder and unzip the files.

Usage

There are three possible ways to run the program:

1.

With the example data uncompressed in data/, you can get the top 50 most common classes with:

python go_processing.py

2.

With the example data uncompressed in data/, you can also specify how many classes to show. For example to get the top 100 classes:

python go_processing.py 100

3.

You can also specify the path to two input files and the number of classes to show. Note however that this program is currently built only for the sample data, so it most likely won't work with other files.

python go_processing.py <file1> <file2> <n>

<file1> should be similar to data/gene_association.mgi
<file2> should be similar to data/mergoGO.out