Pathway-Predictor

Simple python script to predict biological pathways based on protein interaction data from STRING database.

Use: Download, run python src/main.py query_file_path iterations string-db_threshold proteinatlas-db_threshold

string-db_threshold recommended value is 900, proteinatlas-db_threshold recommended value is 1.0.

start_acc and end_acc refer to Accession numbers of proteins as used by Uniprot. ENSG or ENSP headed IDs may also be used. Max distance to explore = 2 x iterations

Please download Protein Atlas Database (proteinatlas.org) and STRING human database (string-db.org), and store them within /data. Ensure that the Protein Atlas Database is proteinatlas.json and the STRING human database is 9606.protein.links.v11.0.txt (you may need to add the .txt extension). The databases are too large to be included within this repo.

/data/conversions.json is cached data from uniprot.org's mapping service between identifiers.