readme.txt

This is a small tutorial

###36261.T_guttata.goa.txt and Zebra_Finch.txt is an example GAF file

This script gets you a significantly differentially expressed list of go terms and genes


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.