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.

Parameters:

  • raw_half_lives (Dict[str, float]) – Dictionary that maps monomer ID’s to their half-lives

  • al. (as reported in Nagar et.) –

Return type:

None

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.

Parameters:

  • symbols_to_monomer_ids (Dict[str, str]) – Dictionary that maps gene symbols to protein

  • model. (monomer ID's used by the) –

Returns:

Dictionary that maps protein monomer ids to their half-lives as reported in Nagar et. al. (2021).

Return type:

id_to_half_life

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.

Return type:

Dict[str, str]