from pyscescbm import CBRead, CBWrite, CBTools
from pyscescbm import CBSolver as slv
### Active script ###
model_file = model_name + '.xml'
data_dir = os.path.join(cDir, 'data', model_name)
model_dir = os.path.join(data_dir,'models','sbml')
work_dir2 = os.path.join(data_dir,'models','h-format')
if not os.path.exists(work_dir2):
os.makedirs(work_dir2)
if sbml_level == 3:
print('Trying level 3')
cmod = CBRead.readSBML3FBC(model_file, work_dir=model_dir)
else:
cmod = CBRead.readSBML2FBA(model_file, work_dir=model_dir)
cmod.id = model_name
print('\nAttempting to delete bounds for biomass reaction,', cmod.getActiveObjective().getFluxObjectiveReactions()[0])
cmod.deleteBoundsForReactionId(cmod.getActiveObjective().getFluxObjectiveReactions()[0])
mLP = slv.analyzeModel(cmod, return_lp_obj=True)
CBWrite.printFBASolution(cmod)
tmp_mid = cmod.id+'_cplex'
CBTools.countedPause(1)
cmod.id = tmp_mid
if not os.path.exists(work_dir):
os.mkdir(work_dir)
if os.listdir(work_dir) == []:
raise UserWarning("No files to analyze in directory {0:s}".format(work_dir))
for file_in in os.listdir(work_dir):
if file_in.endswith('noinf_r.ine.all'):
subnetwork_name = file_in.replace('.noinf_r.ine.all','')
model_file = "{0:s}.xml".format(subnetwork_name)
vertex_file = os.path.join(work_dir, '{0:s}.noinf_r.ine.all'.format(subnetwork_name) )
rfva_file = os.path.join(work_dir, '{0:s}.noinf_r.ine.opt.fva'.format(subnetwork_name) )
if sbml_level == 3:
try:
cmod = CBRead.readSBML3FBC(model_file, work_dir=model_dir)
except:
cmod = CBRead.readSBML2FBA(model_file, work_dir=model_dir)
else:
cmod = CBRead.readSBML2FBA(model_file, work_dir=model_dir)
cmod.id = subnetwork_name
CBTools.addStoichToFBAModel(cmod)
CBTools.processBiGGchemFormula(cmod)
if USE_COLUMN_CROSSCHECK:
mismatch = []
F = open(os.path.join(H_format_dir, '{0:s}.noinf_r.columns.txt'.format(subnetwork_name) ), 'r')
indx_lst = []
for L in F:
l = [i.strip() for i in L.split(',')]
if len(l) == 2:
