def mergeASM(modelfile, outputfile, prefix='exp'):
'''!
Function to read the AdvanceSyn model specification file(s)
and merge them into a single AdvanceSyn model specification
file.
Usage:
python astools.py mergeASM --prefix=exp --modelfile=models/asm/glycolysis.modelspec;models/asm/RFPproduction.modelspec --outputfile=models/asm/glycolysis_RFP.modelspec
@param modelfile String: Relative path(s) to the model specification
file(s), separated by semi-colon.
@param outputfile String: Relative path to the output model
objects file.
@param prefix String: Prefix for new reaction IDs. This prefix
cannot be any existing prefixes in any of the model specifications
to be merged. Default = 'exp'.
'''
specList = []
modelobjList = []
modelfile = [x.strip() for x in modelfile.split(';')]
print('Input Model File(s) ...')
count = 1
for mf in modelfile:
mf = os.path.abspath(mf)
print('ASM Model File %s: %s' % (count, mf))
(spec, modelobj) = modelReader(mf, 'ASM', 'basic')
specList.append(spec)
modelobjList.append(modelobj)
count = count + 1
print('')
(merged_spec, merged_modelobj) = \
ASModeller.modelMerge(specList, modelobjList, prefix,
True, False)
filepath = os.path.abspath(outputfile)
print('Output AdvanceSyn Model Specification File: ' + filepath)
outfile = open(filepath, 'w')
merged_spec.write(outfile)
outfile.close()
def generateModelObject(modelfile, outputfile, prefix='exp'):
'''!
Function to read the AdvanceSyn model specification file(s)
and generate a file consisting of the internal model objects.
Usage:
python astools.py genMO --prefix=exp --modelfile=models/asm/glycolysis.modelspec;models/asm/RFPproduction.modelspec --outputfile=models/mo/glycolysis.mo
@param modelfile String: Relative path(s) to the model specification
file(s), separated by semi-colon.
@param outputfile String: Relative path to the output model
objects file.
@param prefix String: Prefix for new reaction IDs. This prefix
cannot be any existing prefixes in any of the model specifications
to be merged. Default = 'exp'.
'''
specList = []
modelobjList = []
modelfile = [x.strip() for x in modelfile.split(';')]
print('Input Model File(s) ...')
count = 1
for mf in modelfile:
mf = os.path.abspath(mf)
print('ASM Model File %s: %s' % (count, mf))
(spec, modelobj) = modelReader(mf, 'ASM', 'extended')
specList.append(spec)
modelobjList.append(modelobj)
count = count + 1
print('')
(merged_spec, merged_modelobj) = \
ASModeller.modelMerge(specList, modelobjList, prefix,
True, True)
filepath = os.path.abspath(outputfile)
print('Output Model Objects File: ' + filepath)
with open(filepath, 'wb') as f:
dumpdata = (merged_spec, merged_modelobj)
pickle.dump(dumpdata, f, pickle.HIGHEST_PROTOCOL)