def test_run_fba_cobra(self):
print('\n\nThis test fails under Linux.\n\n')
cmod = cbmpy.readCOBRASBML('L2CBR_iJR904.glc.xml', work_dir=MDIR,\
output_dir=self.CDIR, delete_intermediate=True)
cmod2 = cbmpy.readSBML3FBC('L3FBCV1_iJR904.glc.xml',
work_dir=MDIR,
xoptions={'validate': True})
fba1 = cbmpy.doFBA(cmod)
fba2 = cbmpy.doFBA(cmod2)
del cmod, cmod2
assert_almost_equal(fba1, fba2)
f.replace('.correct.xml', '.noinf_r.columns.txt')),
'r')
for l in F:
L = l.split(',')
print(L)
if len(L) == 2:
idmap[L[1].strip()] = int(L[0]) + 1
F.close()
print(idmap)
if sbml_level == 3:
print('Trying level 3')
submod = CBRead.readSBML3FBC(f, work_dir=sbml_dir)
else:
submod = CBRead.readSBML2FBA(f, work_dir=sbml_dir)
if submod is not None:
cbmpy.doFBA(submod)
a, b = cbmpy.doFVA(submod)
output = {}
for r in submod.reactions:
span = abs(r.fva_max - r.fva_min)
rtype = 'VARIABLE'
if span < 1e-10:
rtype = 'FIXED'
if numpy.isinf(
float(r.fva_max)
): #EvP changed because of numpy.inf is not rational
fva_max = float(999999)
else:
fva_max = r.fva_max
S = 'x{} : {} : {} -- {}'.format(idmap[r.getId()], r.fva_min,
fva_max, rtype)
import os, time, numpy
cDir = os.path.dirname(os.path.abspath(os.sys.argv[0]))
import cbmpy as cbm
model_name = 'iAF692.xml'
cmod = cbm.readSBML3FBC(os.path.join(cDir, 'models', model_name))
cmodS = cmod.clone()
cbm.doFBA(cmod)
fva, fvan = cbm.CBMultiCore.runMultiCoreFVA(cmod, procs=4)
cbm.CBWrite.writeFVAtoCSV(fva,
fvan,
model_name.replace('.xml', ''),
fbaObj=cmod)
cbm.writeModelToExcel97(cmod, model_name.replace('.xml', ''))
exch_reactions = cmod.getReactionIds('R_EX_')
dump = []
# reactions are defined back to front so fwd is "o" and and backward is "i"
for xr_ in exch_reactions:
dump.append(cbm.CBTools.splitSingleReversibleReaction(cmodS, xr_, xr_.replace('R_EX_', 'R_EXo_'),\
xr_.replace('R_EX_', 'R_EXi_')))
cbm.doFBA(cmodS)
fva, fvan = cbm.CBMultiCore.runMultiCoreFVA(cmodS, procs=4)
cbm.CBWrite.writeFVAtoCSV(fva,
fvan,
model_name.replace('.xml', '.split'),
fbaObj=cmodS)
cbm.writeSBML3FBC(cmodS, model_name.replace('.xml', '.split.xml'))
cbm.CBWrite.writeModelToExcel97(cmodS, model_name.replace('.xml', '.split'))
print '\nconstraintFiles'
print constraintFiles
# ok now lets set up our model
# let's set up the base model
# 20130628 fixed Mac unicode insanity
sbmlF = str(os.path.join(cDir, 'models', modelFile))
if USE_SBML3:
cmodBase = cbm.CBRead.readSBML3FBC(sbmlF)
else:
cmodBase = cbm.CBRead.readSBML2FBA(sbmlF)
# cbm.CBTools.processSBMLAnnotationNotes(cmodBase, annotation_key='note')
cbm.doFBA(cmodBase)
# here we define a function that will read the constraint files
def readBounds(filename, delimiter=','):
"""
Give the name of a bounds file and it returns a list of tuples: (Rid,lb,ub)
"""
F = file(filename, 'r')
bounds = []
for L in F:
l = L.split(delimiter)
#print l
if l[0].strip().replace('"', '') == 'Reaction ID':
pass
def test_run_L3FBCV2_iJR904(self):
m = 'L3FBCV2_iJR904.glc.xml'
cmod = self.m[m].clone()
res = cbmpy.doFBA(cmod)
del cmod
assert_almost_equal(DATA[m]['FBA'], res)
def test_run_BIGG2_iAF1260(self):
m = 'BIGG2_iAF1260.xml'
cmod = self.m[m].clone()
res = cbmpy.doFBA(cmod)
del cmod
assert_almost_equal(DATA[m]['FBA'], res)
def main():
model = cbm.CBRead.readSBML3FBC('models/Y7.xml')
vmod = Vmod('metabolic_maps/Yeast_7.svg', model)
cbm.doFBA(model)
cbm.doFBAMinSum(model)
vmod.mapFBA(absminval=1e-5, out_file='metabolic_maps/Y7_fba_default.svg')
model.setReactionLowerBound('r_0659', 0.0)
cbm.doFBA(model)
cbm.doFBAMinSum(model)
vmod.mapFBA(absminval=1e-5,
out_file='metabolic_maps/Y7_fba_irreversible_IDH.svg')
FVA = cbm.doFVA(model)
vmod.mapFVA(FVA,
absminval=1e-5,
minspan=1e-5,
out_file='metabolic_maps/Y7_fva.svg')
gene_ids = ['YER081W', 'YIL074C', 'YKL141W']
for gene_id in gene_ids:
model.setGeneInactive(gene_id)
model.updateNetwork()
cbm.doFBA(model)
cbm.doFBAMinSum(model)
vmod.mapFBA(absminval=1e-5,
out_file='metabolic_maps/Y7_fba_Otero_2013_succinate.svg')
# delft stratagy
model = cbm.CBRead.readSBML3FBC('models/Y7.xml')
vmod = Vmod('metabolic_maps/Yeast_7.svg', model)
model.createObjectiveFunction('r_2056')
cbm.doFBA(model)
cbm.doFBAMinSum(model)
vmod.mapFBA(absminval=1e-5,
out_file='metabolic_maps/Y7_fba_succinate_obj_default.svg')
vmod = Vmod('metabolic_maps/Yeast_7delft.svg', model)
model.setReactionLowerBound('r_0659', 0)
model.setReactionBounds('r_0959', 0, 0) # knock out pyruvate decarboxylase
model.createReaction('r_FRDc', name='cytosolic fumarate reductase')
model.createReactionReagent('r_FRDc', 's_0725', -1) # fumarate
model.createReactionReagent('r_FRDc', 's_1203', -1) # NADH
model.createReactionReagent('r_FRDc', 's_1458', 1) # succinate
model.createReactionReagent('r_FRDc', 's_1198', 1) # NAD
model.createReaction('r_PDHc', name='bacterial PDH')
model.createReactionReagent('r_PDHc', 's_1399', -1) # pyruvate
model.createReactionReagent('r_PDHc', 's_1198', -1) # NAD
model.createReactionReagent('r_PDHc', 's_0529', -1) # CoA
model.createReactionReagent('r_PDHc', 's_0373', 1) # Acetyl-CoA
model.createReactionReagent('r_PDHc', 's_1203', 1) # NADH
model.createReactionReagent('r_PDHc', 's_0456', 1) # CO2
model.setReactionLowerBound('r_PDHc', 0)
vmod.mapFBA(absminval=1e-5,
out_file='metabolic_maps/Y7_fba_succinate_obj_delft.svg')
FVA = cbm.doFVA(model)
vmod.mapFVA(FVA,
absminval=1e-5,
minspan=1e-5,
out_file='metabolic_maps/Y7_fva_succinate_obj_delft.svg.svg')