reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat
Extracts protein half-lives from Supplementary Table S2 of Nagar et. al., “Harnessing Machine Learning to Unravel Protein Degradation in Escherichia coli” (2021).
- reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat.build_half_life_table(raw_half_lives)[source]
Builds the protein half-life flat file that is used as raw data for simulations using them. Assigns all proteins with half-lives greater than the arbitrarily chosen MAX_HALF_LIFE as having a half-life of MAX_HALF-LIFE.
- reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat.get_half_lives(symbols_to_monomer_ids)[source]
Reads protein half-lives from Nagar et. al. (2021) and stores them in a dictionary. Any protein listed that does not exist in the model is skipped.
- reconstruction.ecoli.scripts.protein_half_lives.convert_to_flat.get_symbols_to_monomer_ids()[source]
Builds a mapping from gene symbols to the protein monomer IDs, used in later data import functions.
Returns: symbols_to_monomer_ids: Dictionary from gene symbol to first associated protein monomer ID.