Missing PPI network generation script

[slathwal]

Hi team,
The script for ppi data processing ./data/scripts/ppi/export_ppi_all_genes.py, loads data as follows:
path_edge_list = '../../raw/ppi/2022-03-PPI/processed/ppi_edgelist.txt'

However, it is not clear how the file ppi_edgelist.txt has been generated.

The README.md file in the raw data description of ppi folder ./data/raw/ppi/2022-03-PPI/ mentions three data sources, but it's unclear how to get the edgelist file from those sources. Could you please guide me on how PPI generation has been done or add a script to generate ppi_edgelist.txt file from the raw data files mentioned in ppi raw data folder?

[xianglin226]

Thank you for raising this question. We’ve uploaded all the scripts and supporting files to GitHub.
In short:

1. Using hgnc2map.txt (in data/raw/ppi/2022-03-PPI) together with the raw PPI files (links are listed in the same folder), you can run union_ppi.py to generate ppi_edgelist.txt.
2. Then, with geneinfo_beta.txt (in data/raw/ppi/2022-03-PPI) and ppi_edgelist.txt, you can run export_ppi_all_genes.py to build ppi_all_genes_edgelist.txt.

[slathwal]

Hi @xianglin226 Thank you so much for updating the repo. I will check these files out. Really appreciate your response!