gozsari / Go_Propagation

This repository is created to propagate go terms with respect to the go hierarchy in go_basic.obo file

Go_Propagation

This repository is created to propagate go terms with respect to go hierarchy defined in go_basic.obo file by using is_a and part_of relations.

• The following figure shows a sample of Go term hierarchy

Installation

How to run Go_Propagation to obtain the propogation results

Preparation to run Go_Propagation

• Clone the Git Repository

Downloading go_basic.obo !!!

• Due to the periodic updating of the GO term hierarchy, go_basic.obo must be downloaded from here into the Go_Propagation folder to have the latest version of the GO term hierarchy

Input file

• The input file must be located under input_folder.
• It must be in either a txt or cvs format
• The colums of input file muust be seperated with either space, tab or commo.
• First line of input file is assumed to be identification line for each column!

Explanation of Parameters

• --inputFile: gene/protein GO annotation file containing gene/protein ids and go_terms, input file extension should be: .txt or .csv
• --seperator: seperator of input file columns, its default value is space, other options can be tab or commo
• --geneColumn: gene/protein id/accession column number (integer) in the input file, starting index = 0
• --goColumn: go term id column number (integer) in the input file, starting index = 0

A sample command to run Go_Propagation is as follows:

python main.py --inputFile sample_input.txt --seperator tab --geneColumn 1 --goColumn 4

Output file

• The results will be located under output_folder with the name: input_file_name.csv

License

MIT License

Copyright (c) 2021 CanSyL

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.