"""
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
}