5.1.2.1.2. etfba.io.results
Difine classes of analysis results.
5.1.2.1.2.2. Module Contents
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class etfba.io.results.PrettyDict(*args, ndigits=3, **kwargs)[source]
Bases: dict
dict() -> new empty dictionary
dict(mapping) -> new dictionary initialized from a mapping object’s
- dict(iterable) -> new dictionary initialized as if via:
d = {}
for k, v in iterable:
- dict(**kwargs) -> new dictionary initialized with the name=value pairs
in the keyword argument list. For example: dict(one=1, two=2)
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ndigits[source]
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save(file, exp_transform=False)[source]
- Parameters:
file (str) – File ending with .xlsx, .tsv, or .bin format.
log_transform (bool) – Determines whether to apply natural exponential transformation.
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__repr__()[source]
Return repr(self).
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class etfba.io.results.FBAResults(opt_obj, opt_fluxes, opt_success, stoy_mat)[source]
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opt_objective[source]
Optimal objective value achieved during optimization.
- Type:
float
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opt_fluxes[source]
Dictionary mapping reaction ID to its optimal flux value.
- Type:
dict
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optimization_successful[source]
Indicates whether the optimization process was successful.
- Type:
bool
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_opt_obj[source]
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_opt_fluxes[source]
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_opt_success[source]
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_stoy_mat[source]
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property opt_objective[source]
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property opt_fluxes[source]
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property optimization_successful[source]
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statement(metabid)[source]
- Parameters:
metabid (str) – Metabolite ID.
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class etfba.io.results.TFBAResults(opt_obj, opt_fluxes, opt_lnconcs, opt_dgps, opt_success, stoy_mat, **kwargs)[source]
Bases: FBAResults
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...
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opt_concentrations[source]
Dictionary mapping metabolite ID to its optimal concentration.
- Type:
dict
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opt_directions[source]
Dictionary mapping reaction ID to its direction (“f” for forward, “b” for
backward).
- Type:
dict
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opt_gibbs_energy[source]
Dictionary mapping reaction ID to its optimal deltaGprime value.
- Type:
dict
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_opt_lnconcs[source]
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_opt_concs[source]
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_opt_dgps[source]
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property opt_concentrations[source]
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property opt_directions[source]
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property opt_gibbs_energy[source]
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class etfba.io.results.EFBAResults(opt_obj, opt_fluxes, opt_total_epc, opt_epcs, opt_success, stoy_mat, **kwargs)[source]
Bases: FBAResults
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...
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opt_total_enzyme_cost[source]
Optimal total enzyme protein cost achieved.
- Type:
float
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opt_enzyme_costs[source]
Dictionary mapping reaction ID to its optimal enzyme protein abundance.
- Type:
dict
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_opt_total_epc[source]
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_opt_epcs[source]
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property opt_total_enzyme_cost[source]
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property opt_enzyme_costs[source]
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class etfba.io.results.ETFBAResults(opt_obj, opt_fluxes, opt_lnconcs, opt_dgps, opt_total_epc, opt_epcs, opt_success, stoy_mat)[source]
Bases: TFBAResults, EFBAResults
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...
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class etfba.io.results.VariabilityResults(obj_value, gamma, ranges)[source]
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objective_value[source]
Objective value obtained from TFBA, EFBA, or ETFBA analysis.
- Type:
float
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gamma[source]
Control parameter for the objective value.
- Type:
float
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_obj_value[source]
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_gamma[source]
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_ranges[source]
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property objective_value[source]
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property gamma[source]
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class etfba.io.results.FVAResults(obj_value, gamma, ranges)[source]
Bases: VariabilityResults
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...
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flux_ranges[source]
Dictionary containing reaction IDs mapped to their corresponding net flux
ranges [lb, ub].
- Type:
dict
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property flux_ranges[source]
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class etfba.io.results.TVAResults(obj_value, gamma, ranges)[source]
Bases: VariabilityResults
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...
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gibbs_energy_ranges[source]
Dictionary containing reaction IDs mapped to their corresponding ranges of
deltaGprime [lb, ub].
- Type:
dict
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property gibbs_energy_ranges[source]
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class etfba.io.results.EVAResults(obj_value, gamma, ranges)[source]
Bases: VariabilityResults
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...
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protein_cost_ranges[source]
Dictionary mapping reaction IDs to their respective ranges of protein cost
[lb, ub].
- Type:
dict
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property protein_cost_ranges[source]