def extractCompartmentStatistics(bioNumber,useID,reactionDefinitions,speciesEquivalence):
'''
Iterate over the translated species and check which compartments
are used together, and how.
'''
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.pathwaycommons = False
#call the atomizer (or not)
#if atomize:
translator,onlySynDec = mc.transformMolecules(parser,database,reactionDefinitions,speciesEquivalence)
#else:
# translator={}
compartmentPairs = {}
for element in translator:
temp = extractCompartmentCoIncidence(translator[element])
for element in temp:
if element not in compartmentPairs:
compartmentPairs[element] = temp[element]
else:
compartmentPairs[element].update(temp[element])
finalCompartmentPairs = {}
print '-----'
for element in compartmentPairs:
if element[0][0] not in finalCompartmentPairs:
finalCompartmentPairs[element[0][0]] = {}
finalCompartmentPairs[element[0][0]][tuple([element[0][1],element[1][1]])] = compartmentPairs[element]
return finalCompartmentPairs
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
pathwaycommons = False
if bioGrid:
loadBioGrid()
database = structures.Databases()
database.forceModificationFlag = True
database.pathwaycommons = False
if pathwaycommons:
database.pathwaycommons = True
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, pathwaycommons=False):
'''
one of the library's main entry methods. Process data from a file
'''
'''
import cProfile, pstats, StringIO
pr = cProfile.Profile()
pr.enable()
'''
setupLog(outputFile + '.log', logging.DEBUG)
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
if document.getModel() == None:
print 'File {0} could not be recognized as a valid SBML file'.format(bioNumber)
return
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.forceModificationFlag = True
database.pathwaycommons = pathwaycommons
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.)
'''
pr.disable()
s = StringIO.StringIO()
sortby = 'cumulative'
ps = pstats.Stats(pr, stream=s).sort_stats(sortby)
ps.print_stats(10)
print s.getvalue()
'''
database.document = document
database.reactionDefinitions = reactionDefinitions
database.useID = useID
database.speciesEquivalence = speciesEquivalence
database.atomize = atomize
returnArray = analyzeHelper(document, reactionDefinitions, useID, outputFile, speciesEquivalence, atomize, translator)
with open(outputFile, 'w') as f:
f.write(returnArray.finalString)
#with open('{0}.dict'.format(outputFile),'wb') as f:
# pickle.dump(returnArray[-1],f)
if atomize and onlySynDec:
returnArray = list(returnArray)
#returnArray.translator = -1
returnArray = AnalysisResults(*(list(returnArray[0:-1]) + [database]))
return returnArray
def readFromString(inputString,reactionDefinitions,useID,speciesEquivalence=None,atomize=False, loggingStream=None):
'''
one of the library's main entry methods. Process data from a string
'''
console = None
if loggingStream:
console = logging.StreamHandler(loggingStream)
console.setLevel(logging.DEBUG)
setupStreamLog(console)
reader = libsbml.SBMLReader()
document = reader.readSBMLFromString(inputString)
parser =SBML2BNGL(document.getModel(),useID)
bioGrid = False
pathwaycommons = True
if bioGrid:
loadBioGrid()
database = structures.Databases()
database.assumptions = defaultdict(set)
database.document = document
database.forceModificationFlag = True
database.reactionDefinitions = reactionDefinitions
database.useID = useID
database.atomize = atomize
database.speciesEquivalence = speciesEquivalence
database.pathwaycommons = True
database.isConversion = True
#if pathwaycommons:
# database.pathwaycommons = True
namingConventions = resource_path('config/namingConventions.json')
if atomize:
translator,onlySynDec = mc.transformMolecules(parser,database,reactionDefinitions,namingConventions,speciesEquivalence,bioGrid)
database.species = translator.keys()
else:
translator={}
#logging.getLogger().flush()
if loggingStream:
finishStreamLog(console)
returnArray = analyzeHelper(document, reactionDefinitions,
useID,'', speciesEquivalence, atomize, translator, database)
if atomize and onlySynDec:
returnArray = list(returnArray)
returnArray = AnalysisResults(*(list(returnArray[0:-2]) + [database] + [returnArray[-1]]))
return returnArray
def analyzeFile(bioNumber,reactionDefinitions,useID,namingConventions,outputFile,
speciesEquivalence=None,atomize=False,bioGrid=False,pathwaycommons=False):
'''
one of the library's main entry methods. Process data from a file
'''
'''
import cProfile, pstats, StringIO
pr = cProfile.Profile()
pr.enable()
'''
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
parser =SBML2BNGL(document.getModel(),useID)
database = structures.Databases()
database.forceModificationFlag = True
database.pathwaycommons = pathwaycommons
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.)
'''
pr.disable()
s = StringIO.StringIO()
sortby = 'cumulative'
ps = pstats.Stats(pr, stream=s).sort_stats(sortby)
ps.print_stats(10)
print s.getvalue()
'''
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, pathwaycommons=False, ignore=False, noConversion=False):
'''
one of the library's main entry methods. Process data from a file
'''
'''
import cProfile, pstats, StringIO
pr = cProfile.Profile()
pr.enable()
'''
setupLog(outputFile + '.log', logging.DEBUG)
logMess.log = []
logMess.counter = -1
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(bioNumber)
if document.getModel() == None:
print 'File {0} could not be recognized as a valid SBML file'.format(bioNumber)
return
parser =SBML2BNGL(document.getModel(),useID)
parser.setConversion(not noConversion)
database = structures.Databases()
database.assumptions = defaultdict(set)
database.forceModificationFlag = True
database.pathwaycommons = pathwaycommons
database.ignore = ignore
database.assumptions = defaultdict(set)
bioGridDict = {}
if bioGrid:
bioGridDict = loadBioGrid()
translator = {}
# 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
try:
if atomize:
translator, onlySynDec = mc.transformMolecules(parser, database, reactionDefinitions,
namingConventions, speciesEquivalence, bioGrid)
except TranslationException as e:
print "Found an error in {0}. Check log for more details. Use -I to ignore translation errors".format(e.value)
if len(logMess.log) > 0:
with open(outputFile + '.log', 'w') as f:
for element in logMess.log:
f.write(element + '\n')
return
# process other sections of the sbml file (functions reactions etc.)
'''
pr.disable()
s = StringIO.StringIO()
sortby = 'cumulative'
ps = pstats.Stats(pr, stream=s).sort_stats(sortby)
ps.print_stats(10)
print s.getvalue()
'''
database.document = document
database.reactionDefinitions = reactionDefinitions
database.useID = useID
database.speciesEquivalence = speciesEquivalence
database.atomize = atomize
database.isConversion = not noConversion
returnArray = analyzeHelper(document, reactionDefinitions, useID, outputFile, speciesEquivalence, atomize, translator, database)
with open(outputFile, 'w') as f:
f.write(returnArray.finalString)
#with open('{0}.dict'.format(outputFile),'wb') as f:
# pickle.dump(returnArray[-1],f)
if atomize and onlySynDec:
returnArray = list(returnArray)
#returnArray.translator = -1
returnArray = AnalysisResults(*(list(returnArray[0:-2]) + [database] + [returnArray[-1]]))
return returnArray
