`ecoli.variants.new_gene_internal_shift`

ecoli.variants.new_gene_internal_shift.apply_variant(sim_data, params)[source]

Modify sim_data so new gene expression and translation efficiency are modified for certain generation ranges.

Parameters:

sim_data (SimulationDataEcoli) – Simulation data to modify

Parameter dictionary of the following format:

{
    # Generation to induce new gene expression
    "induction_gen": Optional(int),
    "exp_trl_eff": {
        # Factor by which to multiply new gene expression once induced
        "exp": float,
        # Translation efficiency for new gene once induced
        "trl_eff": float,
    }
    # Generation to knock out new gene expression (> induction gen)
    "knockout_gen": Optional(int),
    # Environmental condition: "basal", "with_aa", "acetate",
    # "succinate", "no_oxygen"
    "condition": str,
}

Returns:

Simulation data with the following attributes modified:

sim_data.condition
sim_data.external_state.current_timeline_id
# Mapping of generation number to function that takes sim_data
# as first argument and optional extra arguments contained in a
# tuple that will be star expanded. Here, modify_new_gene_exp_trl
# takes two extra arguments: expression and translation_efficiency.
sim_data.internal_shift_dict

Return type:

SimulationDataEcoli

ecoli.variants.new_gene_internal_shift.get_new_gene_ids_and_indices(sim_data)[source]

Determines the indices of new gene cistrons and proteins using the new gene flag in sim_data.

Returns:

4-element tuple containing

new_gene_cistron_ids: names of new gene cistrons
new_gene_indices: indices in rna_data table for new gene cistrons
new_monomer_ids: names of new gene monomers
new_monomer_indices: indices in monomer_data table for new monomers

Parameters:

sim_data (SimulationDataEcoli)

Return type:

tuple[list[str], list[int], list[str], list[int]]

ecoli.variants.new_gene_internal_shift.modify_new_gene_exp_trl(sim_data, expression, translation_efficiency)[source]

Sets expression and translation effiencies of new genes. Modifies:

sim_data.process.transcription.rna_synth_prob
sim_data.process.transcription.rna_expression
sim_data.process.transcription.exp_free
sim_data.process.transcription.exp_ppgpp
sim_data.process.transcription.attenuation_basal_prob_adjustments
sim_data.process.transcription_regulation.basal_prob
sim_data.process.transcription_regulation.delta_prob
sim_data.process.translation.translation_efficiencies_by_monomer

Parameters:

sim_data (SimulationDataEcoli) – Simulation data
expression (float) – Factor by which to adjust new gene expression levels
translation_efficiency (float) – Translation efficiency for new genes

ecoli.variants.new_gene_internal_shift

`ecoli.variants.new_gene_internal_shift`