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Fix FVA in summary calls #525

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merged 3 commits into from
Jun 19, 2017
Merged

Fix FVA in summary calls #525

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cbbde9b
fixing metabolite summary
pstjohn Jun 15, 2017
f236e90
model fva fix
pstjohn Jun 15, 2017
fcfbf7d
pep8 fixes
pstjohn Jun 15, 2017
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12 changes: 8 additions & 4 deletions cobra/flux_analysis/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,11 +54,13 @@ def metabolite_summary(met, threshold=0.01, fva=False, floatfmt='.3g',
flux_summary.index = flux_summary["id"]
flux_summary["maximum"] = zeros(len(rxn_id))
flux_summary["minimum"] = zeros(len(rxn_id))
for rxn in met.reactions:
for rid, rxn in zip(rxn_id, met.reactions):
imax = rxn.metabolites[met] * fva_results.loc[rxn.id, "maximum"]
imin = rxn.metabolites[met] * fva_results.loc[rxn.id, "minimum"]
flux_summary["fmax"] = imax if abs(imin) <= abs(imax) else imin
flux_summary["fmin"] = imin if abs(imin) <= abs(imax) else imax
flux_summary.loc[rid, "fmax"] = (imax if abs(imin) <= abs(imax)
else imin)
flux_summary.loc[rid, "fmin"] = (imin if abs(imin) <= abs(imax)
else imax)

assert flux_summary.flux.sum() < 1E-6, "Error in flux balance"

Expand Down Expand Up @@ -206,11 +208,13 @@ def _process_flux_dataframe(flux_dataframe, fva, threshold, floatfmt):
(flux_dataframe.fmin.abs() > threshold) |
(flux_dataframe.fmax.abs() > threshold)].copy()

flux_dataframe.loc[flux_dataframe.flux.abs() < threshold, 'flux'] = 0

# Make all fluxes positive
if not fva:
flux_dataframe['is_input'] = flux_dataframe.flux >= 0
flux_dataframe.flux = \
flux_dataframe.flux.abs().astype('float').round(6)
flux_dataframe.flux.abs().astype('float')
else:

def get_direction(flux, fmin, fmax):
Expand Down