def readModel(file, maxDelete, bio_reaction, infinityValue, USE_GENE):
"""
Function that reads in a model from SBML3 file
Optional: function GrowthCondition.setCondition for setting flux values
to mimic growth conditions
- *file* sbml filename
- *bio_reaction* inner objective, usually biomass reaction
- *lp* primal LP, derived from model
- *splitCouples* list from reversible reactions that are split
- *lpName* name for LP, derived from filename
- *GPRdict* dictionary with (iso)enzymes mapped to reactions
- *SubUdict* dictionary with genes mapped to isoenzymes
- *Scale* upscale factor
- *maxDelete* maximum gene/reaction deletions allowed
- *infinityValue* boundary values that can be assumed infinite
"""
# Read in model and set growth conditions
model = cbm.CBRead.readSBML3FBC('Models/' + file)
# remove equiliy bonds
model.splitEqualityFluxBounds()
model.setObjectiveFlux(bio_reaction, osense='maximize')
lpName = file.replace('.xml', '')
lpName = lpName.replace('SynthSinks/', '')
#model = GrowthCondition.setCondition(model, bio_reaction)
cbm.analyzeModel(model)
# Build dictionaries for GPR associations
GPRdict = {}
SubUdict = {}
if USE_GENE:
GPRdict, SubUdict = doGeneMapping(model)
# Upscale reaction boundaries, if needed
model, Scale = upscaleModel(model)
infinityValue = infinityValue * Scale
# Write LP
cbm.CBWrite.writeModelLP(model, work_dir='LPs', fname=lpName + '_primal')
lp = cplex.Cplex('LPs/' + lpName + '_primal.lp')
return lp, lpName, GPRdict, SubUdict, Scale, maxDelete, infinityValue
def readModel(file, maxDelete, bio_reaction, infinityValue, USE_GENE):
"""
Function that reads in a model from SBML3 file
Optional: function GrowthCondition.setCondition for setting flux values
to mimic growth conditions
- *file* sbml filename
- *bio_reaction* inner objective, usually biomass reaction
- *lp* primal LP, derived from model
- *splitCouples* list from reversible reactions that are split
- *lpName* name for LP, derived from filename
- *GPRdict* dictionary with (iso)enzymes mapped to reactions
- *SubUdict* dictionary with genes mapped to isoenzymes
- *Scale* upscale factor
- *maxDelete* maximum gene/reaction deletions allowed
- *infinityValue* boundary values that can be assumed infinite
"""
# Read in model and set growth conditions
model = cbm.CBRead.readSBML3FBC(file)
# remove equiliy bonds
model.splitEqualityFluxBounds()
model.setObjectiveFlux(bio_reaction, osense='maximize')
lpName = file.replace('.xml', '')
#model = GrowthCondition.setCondition(model, bio_reaction)
cbm.analyzeModel(model)
# Build dictionaries for GPR associations
GPRdict = {}
SubUdict = {}
if USE_GENE:
GPRdict, SubUdict= doGeneMapping(model)
# Upscale reaction boundaries, if needed
model, Scale = upscaleModel(model)
infinityValue = infinityValue * Scale
# Write LP
cbm.CBWrite.writeModelLP(model, fname = 'Original')
lp = cplex.Cplex('Original.lp')
return lp, lpName, GPRdict, SubUdict, Scale, maxDelete, infinityValue