ecoli.analysis.multivariant.average_monomer_counts

Anaylsis Script for saving all protein counts impacted by new genes. Note that this file only works for saving data for simulations that contain at least two variants (one control and one experimental variant).

ecoli.analysis.multivariant.average_monomer_counts.IGNORE_FIRST_N_GENS = 1

Indicate which generation the data should start being collected from (sometimes this number should be greater than 0 because the first few generations may not be representative of the true dynamics occuring in the cell).

ecoli.analysis.multivariant.average_monomer_counts.plot(params, conn, history_sql, config_sql, sim_data_dict, validation_data_paths, outdir, variant_metadata, variant_names)

Calculates average monomer counts per variant and saves them as separate files under {outdir}/saved_data/unfiltered_data. Filters data to only include monomers whose counts are greater than params["filter_num"] (default 0) and saves under {outdir}/saved_data/filtered_data.

Parameters:

• params (dict[str, Any])

• conn (DuckDBPyConnection)

• history_sql (str)

• config_sql (str)

• sim_data_dict (dict[str, dict[int, str]])

• validation_data_paths (list[str])

• outdir (str)

• variant_metadata (dict[str, dict[int, Any]])

• variant_names (dict[str, str])

ecoli.analysis.multivariant.average_monomer_counts.save_file(out_dir, filename, columns, values)