##This is a small tutorial. This script gets you a significantly differentially expressed list of go terms and genes
36261.T_guttata.goa.txt.gz and Zebra_Finch.txt is an example GAF file. It must be unzipped before use (gunzip 36261.T_guttata.goa.txt.gz).
In order to run this script you must first obtain a GAF file from the link below for you desired dataset.
https://www.ebi.ac.uk/GOA/proteomes
You will then run the command below to generate a mapping file python3 GAF_To_GO_Map.py file_name
###Example
python3 GAF_To_GO_Map.py 36261.T_guttata.goa.txt
This will produce a file called Gene2Term.txt which will be the input file for the R script below.
You will also need a file resembling Zebra_Finch.txt containing your expermiental differential expression data.
You will then follow either TopGO_Script.R or TopGO_Scrpt.pdf which has the steps and comments to walk you through it.
The final product of this script will be an array called go2Gene that contains the GO:ID, number of annotated genes and a list of the gene symbols and a graph of the three most significant nodes and their parents.