Source code for reconstruction.ecoli.dataclasses.adjustments

"""
Simulation data manual adjustments necessary for proper metabolism.

Raw tsv files in 'reconstruction/ecoli/flat/adjustments'

"""


[docs] class Adjustments(object): def __init__(self, raw_data): self._add_adjustments(raw_data)
[docs] def _add_adjustments(self, raw_data): self.translation_efficiencies_adjustments = { adj["name"]: adj["value"] for adj in raw_data.adjustments.translation_efficiencies_adjustments } self.balanced_translation_efficiencies = [ adj["proteins"] for adj in raw_data.adjustments.balanced_translation_efficiencies ] self.rna_expression_adjustments = { adj["name"]: adj["value"] for adj in raw_data.adjustments.rna_expression_adjustments } self.rna_deg_rates_adjustments = { adj["name"]: adj["value"] for adj in raw_data.adjustments.rna_deg_rates_adjustments } self.protein_deg_rates_adjustments = { adj["name"]: ( adj["value"] if not isinstance(adj["value"], str) else eval(adj["value"]) ) # eval fractions for adj in raw_data.adjustments.protein_deg_rates_adjustments } self.relative_metabolite_concentrations_changes = { adj["media"]: {adj["metabolite"]: adj["fold_change"]} for adj in raw_data.adjustments.relative_metabolite_concentrations_changes }