def summary(self, solution=None, threshold=0.01, fva=None, names=False,
floatfmt='.3g'):
"""
Print a summary of the production and consumption fluxes.
This method requires the model for which this metabolite is a part
to be solved.
Parameters
----------
solution : cobra.Solution, optional
A previously solved model solution to use for generating the
summary. If none provided (default), the summary method will
resolve the model. Note that the solution object must match the
model, i.e., changes to the model such as changed bounds,
added or removed reactions are not taken into account by this
method.
threshold : float, optional
Threshold below which fluxes are not reported.
fva : pandas.DataFrame, float or None, optional
Whether or not to include flux variability analysis in the output.
If given, fva should either be a previous FVA solution matching
the model or a float between 0 and 1 representing the
fraction of the optimum objective to be searched.
names : bool, optional
Emit reaction and metabolite names rather than identifiers (default
False).
floatfmt : string, optional
Format string for floats (default '.3g').
"""
from cobra.flux_analysis.summary import metabolite_summary
return metabolite_summary(self, solution=solution, threshold=threshold,
fva=fva, names=names, floatfmt=floatfmt)
def summary(self, solution=None, threshold=0.01, fva=False,
floatfmt='.3g'):
"""Print a summary of the reactions which produce and consume this
metabolite.
This method requires the model for which this metabolite is a part
to be solved.
Parameters
----------
solution : cobra.core.Solution
A previously solved model solution to use for generating the
summary. If none provided (default), the summary method will
resolve the model. Note that the solution object must match the
model, i.e., changes to the model such as changed bounds,
added or removed reactions are not taken into account by this
method.
threshold : float
a value below which to ignore reaction fluxes
fva : float (0->1), or None
Whether or not to include flux variability analysis in the output.
If given, fva should be a float between 0 and 1, representing the
fraction of the optimum objective to be searched.
floatfmt : string
format method for floats, passed to tabulate. Default is '.3g'.
"""
from cobra.flux_analysis.summary import metabolite_summary
return metabolite_summary(self, solution=solution, threshold=threshold,
fva=fva, floatfmt=floatfmt)
def summary(self,
solution=None,
threshold=0.01,
fva=None,
names=False,
floatfmt='.3g'):
"""
Print a summary of the production and consumption fluxes.
This method requires the model for which this metabolite is a part
to be solved.
Parameters
----------
solution : cobra.Solution, optional
A previously solved model solution to use for generating the
summary. If none provided (default), the summary method will
resolve the model. Note that the solution object must match the
model, i.e., changes to the model such as changed bounds,
added or removed reactions are not taken into account by this
method.
threshold : float, optional
Threshold below which fluxes are not reported.
fva : pandas.DataFrame, float or None, optional
Whether or not to include flux variability analysis in the output.
If given, fva should either be a previous FVA solution matching
the model or a float between 0 and 1 representing the
fraction of the optimum objective to be searched.
names : bool, optional
Emit reaction and metabolite names rather than identifiers (default
False).
floatfmt : string, optional
Format string for floats (default '.3g').
"""
from cobra.flux_analysis.summary import metabolite_summary
return metabolite_summary(self,
solution=solution,
threshold=threshold,
fva=fva,
names=names,
floatfmt=floatfmt)
def summary(self, threshold=0.01, fva=False, floatfmt='.3g', **kwargs):
"""Print a summary of the reactions which produce and consume this
metabolite.
This method requires the model for which this metabolite is a part
to be solved.
Parameters
----------
threshold : float
a value below which to ignore reaction fluxes
fva : float (0->1), or None
Whether or not to include flux variability analysis in the output.
If given, fva should be a float between 0 and 1, representing the
fraction of the optimum objective to be searched.
floatfmt : string
format method for floats, passed to tabulate. Default is '.3g'.
"""
from cobra.flux_analysis.summary import metabolite_summary
return metabolite_summary(self, threshold=threshold, fva=fva,
floatfmt=floatfmt, **kwargs)