def readFromString(inputString,
reactionDefinitions,
useID,
speciesEquivalence=None,
atomize=False):
'''
one of the library's main entry methods. Process data from a string
'''
try:
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(inputString)
parser = SBML2BNGL(document.getModel(), useID)
bioGrid = False
if bioGrid:
loadBioGrid()
database = structures.Databases()
namingConventions = resource_path('config/namingConventions.json')
if atomize:
translator, onlySynDec = mc.transformMolecules(
parser, database, reactionDefinitions, namingConventions,
speciesEquivalence, bioGrid)
else:
translator = {}
return analyzeHelper(document, reactionDefinitions, useID, '',
speciesEquivalence, atomize, translator)[-2]
except:
return -5
def analyzeFile(bioNumber,reactionDefinitions,useID,namingConventions,outputFile,
speciesEquivalence=None,atomize=False,bioGrid=False):
'''
one of the library's main entry methods. Process data from a string
'''
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
#call the atomizer (or not)
bioGridDict = {}
if bioGrid:
bioGridDict = loadBioGrid()
if atomize:
translator = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid)
else:
translator={}
returnArray= analyzeHelper(document,reactionDefinitions,useID,outputFile,speciesEquivalence,atomize,translator)
with open(outputFile,'w') as f:
f.write(returnArray[-2])
#with open('{0}.dict'.format(outputFile),'wb') as f:
# pickle.dump(returnArray[-1],f)
return returnArray[0:-2]
def readFromString(inputString,reactionDefinitions,useID,speciesEquivalence=None,atomize=False):
'''
one of the library's main entry methods. Process data from a string
'''
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(inputString)
parser =SBML2BNGL(document.getModel(),useID)
bioGrid = False
if bioGrid:
loadBioGrid()
database = structures.Databases()
namingConventions = 'config/namingConventions.json'
if atomize:
translator = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid)
else:
translator={}
return analyzeHelper(document,reactionDefinitions,useID,'',speciesEquivalence,atomize,translator)[-2]
def analyzeFile(bioNumber,
reactionDefinitions,
useID,
namingConventions,
outputFile,
speciesEquivalence=None,
atomize=False,
bioGrid=False):
'''
one of the library's main entry methods. Process data from a file
'''
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
parser = SBML2BNGL(document.getModel(), useID)
database = structures.Databases()
database.forceModificationFlag = True
bioGridDict = {}
if bioGrid:
bioGridDict = loadBioGrid()
#call the atomizer (or not). structured molecules are contained in translator
#onlysyndec is a boolean saying if a model is just synthesis of decay reactions
if atomize:
translator, onlySynDec = mc.transformMolecules(parser, database,
reactionDefinitions,
namingConventions,
speciesEquivalence,
bioGrid)
else:
translator = {}
#process other sections of the sbml file (functions reactions etc.)
returnArray = analyzeHelper(document, reactionDefinitions, useID,
outputFile, speciesEquivalence, atomize,
translator)
with open(outputFile, 'w') as f:
f.write(returnArray[-2])
#with open('{0}.dict'.format(outputFile),'wb') as f:
# pickle.dump(returnArray[-1],f)
if atomize and onlySynDec:
returnArray = list(returnArray)
returnArray[0] = -1
return tuple(returnArray[0:-2])
def analyzeFile(bioNumber,reactionDefinitions,useID,namingConventions,outputFile,
speciesEquivalence=None,atomize=False,bioGrid=False):
'''
one of the library's main entry methods. Process data from a file
'''
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.forceModificationFlag = True
bioGridDict = {}
if bioGrid:
bioGridDict = loadBioGrid()
#call the atomizer (or not). structured molecules are contained in translator
#onlysyndec is a boolean saying if a model is just synthesis of decay reactions
if atomize:
translator,onlySynDec = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid)
else:
translator={}
#process other sections of the sbml file (functions reactions etc.)
returnArray= analyzeHelper(document,reactionDefinitions,useID,outputFile,speciesEquivalence,atomize,translator)
with open(outputFile,'w') as f:
f.write(returnArray[-2])
#with open('{0}.dict'.format(outputFile),'wb') as f:
# pickle.dump(returnArray[-1],f)
if atomize and onlySynDec:
returnArray = list(returnArray)
returnArray[0] = -1
return tuple(returnArray[0:-2])
