def processMDLR(self, mdlrPath):
'''
main method. extracts species definition, creates bng-xml, creates mdl definitions
'''
nautyDict = self.xml2HNautySpeciesDefinitions(mdlrPath)
#append extended bng-xml to the bng-xml definition (the one that doesn't include seed information)
bngxmlestr = writeBXe.mergeBXBXe(namespace.input + '_total.xml', namespace.input + '_extended.xml')
with open(mdlrPath + '_total.xml', 'w') as f:
f.write(bngxmlestr)
xmlspec = readBNGXML.parseFullXML(namespace.input + '.xml')
# write out the equivalent plain mdl stuffs
mdlDict = writeMDL.constructMCell(xmlspec, namespace.input, finalName.split(os.sep)[-1], nautyDict)
writeMDL.writeMDL(mdlDict, finalName)
def extractStatsFromFile(fileName):
fileStats = {}
structures = bxml.parseFullXML(fileName)
fileStats['compression'] = 1 - len(structures['molecules'])*1.0/len(structures['observables']) \
if len(structures['observables']) > 0 else 0
fileStats['index'] = fileName.split('/')[-1].split('.')[0]
fileStats['nreactions'] = len(structures['rules'])
fileStats['nspecies'] = len(structures['observables'])
if fileStats['nreactions'] > 0:
fileStats['atomization'] = sum([
1 for x in structures['rules']
if any([y.action not in ['Add', 'Delete'] for y in x[0].actions])
]) * 1.0 / len(structures['rules'])
else:
fileStats['atomization'] = 0
return fileStats
normalizeMoleculeNamespace(molecule, moleculeSettings)
for product in ruleDescription[0].products:
for molecule in product.molecules:
for moleculeSettings in normalizationSettings['molecules']:
normalizeMoleculeNamespace(molecule, moleculeSettings)
def defineConsole():
"""
defines the program console line commands
"""
parser = argparse.ArgumentParser(description='SBML to BNGL translator')
parser.add_argument('-n', '--normalize', type=str, help='normalization settings file', required=True)
return parser
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
with open(namespace.normalize) as f:
normalizationSettings = yaml.load(f)
for model in normalizationSettings['model']:
bnglNamespace = readBNGXML.parseFullXML(model['name'])
normalizeNamespace(bnglNamespace, model)
bnglString = readBNGXML.createBNGLFromDescription(bnglNamespace)
with open(model['name']+ '_norm.bngl','w') as f:
f.write(bnglString)
normalizeMoleculeNamespace(molecule, moleculeSettings)
def defineConsole():
"""
defines the program console line commands
"""
parser = argparse.ArgumentParser(description='SBML to BNGL translator')
parser.add_argument('-n',
'--normalize',
type=str,
help='normalization settings file',
required=True)
return parser
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
with open(namespace.normalize) as f:
normalizationSettings = yaml.load(f)
for model in normalizationSettings['model']:
bnglNamespace = readBNGXML.parseFullXML(model['name'])
normalizeNamespace(bnglNamespace, model)
bnglString = readBNGXML.createBNGLFromDescription(bnglNamespace)
with open(model['name'] + '_norm.bngl', 'w') as f:
f.write(bnglString)
for element in [x for x in stdDictionary2[0] if x in intersectingNamespace]:
for state in stdDictionary2[0][element]:
intersectionSpace2[element].add(frozenset(x for x in state if x[0] in lowerIntersectionNamespace))
for element in intersectionSpace:
scoreDict[element]['file2'] = len(intersectionSpace2[element])
for element in intersectionSpace:
scoreDict[element]['intersection'] = [len(intersectionSpace[element] - intersectionSpace2[element]), len(intersectionSpace2[element] - intersectionSpace[element])]
scoreDict[element]['score'] = 1 - scoreDict[element]['intersection'][0]*1.0/scoreDict[element]['file1']
scoreDict[element]['score2'] = 1 - scoreDict[element]['intersection'][1]*1.0/scoreDict[element]['file2']
return scoreDict
def evaluateSimilarity(bnglNamespace, bnglNamespace2):
similarity = {}
similarity['structure'] = evaluateStructureSimilarity(bnglNamespace['molecules'], bnglNamespace2['molecules'])
similarity['process'] = evaluateProcessSimilarity(bnglNamespace, bnglNamespace2)
return similarity
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
bnglNamespace = readBNGXML.parseFullXML(namespace.filename1)
bnglNamespace2 = readBNGXML.parseFullXML(namespace.filename2)
evaluateSimilarity(bnglNamespace, bnglNamespace2)
def reactionBasedAtomizationDistro(directory):
'''
calculates a rection atomization based metric:
ration of atomized reactions (non syndeg) in a model
'''
syndelArray = []
atomizedDistro = []
nonAtomizedDistro = []
atomizationDB = pandas.DataFrame()
# generate bng-xml
# generateBNGXML(directory)
print 'reading bng-xml files'
xmlFiles = getValidFiles(directory, 'xml')
print 'analyzing {0} bng-xml files'.format(len(xmlFiles))
progress = progressbar.ProgressBar()
validFiles = 0
for i in progress(range(len(xmlFiles))):
xml = xmlFiles[i]
# for xml in xmlFiles:
try:
# console.bngl2xml('complex/output{0}.bngl'.format(element),timeout=10)
try:
structures = readBNGXML.parseFullXML(xml)
rules = structures['rules']
observables = structures['observables']
molecules = structures['molecules']
except IOError:
print xml
continue
atomizedProcesses, weight = reactionBasedAtomization(rules)
ato, nonato = stoichiometryAnalysis(rules)
atomizedDistro.extend(ato)
nonAtomizedDistro.extend(nonato)
# if (2,1) in nonato:
# interesting.append(element)
score = atomizedProcesses * 1.0 / weight if weight != 0 else 0
#totalRatomizedProcesses += atomizedProcesses
#totalReactions += len(rules)
#totalProcesses += weight
# calculate yield
activeMolecules = extractActiveMolecules(rules)
activeMoleculeTypes = [x for x in molecules if x.name in activeMolecules]
yieldValue = len([x for x in activeMoleculeTypes if len(
x.components) > 0]) * 1.0 / len(activeMoleculeTypes) if len(activeMoleculeTypes) > 0 else 0
# syndel value
syndelValue = 1 - (len(rules) - weight) * 1.0 / len(rules) if len(rules) > 0 else 0
atomizationDB.set_value(xml, 'score', score)
atomizationDB.set_value(xml, 'weight', weight)
atomizationDB.set_value(xml, 'length', len(rules))
atomizationDB.set_value(xml, 'yild', yieldValue)
atomizationDB.set_value(xml, 'syndel', syndelValue)
atomizationDB.set_value(xml, 'numspecies', len(observables))
validFiles += 1
except IOError:
print 'io'
continue
print 'found {0} models i could extract info from'.format(validFiles)
return atomizationDB
def getModelStructures(bngxml):
structures = readBNGXML.parseFullXML(bngxml)
return structures
normalizeMoleculeNamespace(molecule, moleculeSettings)
def defineConsole():
"""
defines the program console line commands
"""
parser = argparse.ArgumentParser(description="SBML to BNGL translator")
parser.add_argument("-n",
"--normalize",
type=str,
help="normalization settings file",
required=True)
return parser
if __name__ == "__main__":
parser = defineConsole()
namespace = parser.parse_args()
with open(namespace.normalize) as f:
normalizationSettings = yaml.load(f)
for model in normalizationSettings["model"]:
bnglNamespace = readBNGXML.parseFullXML(model["name"])
normalizeNamespace(bnglNamespace, model)
bnglString = readBNGXML.createBNGLFromDescription(bnglNamespace)
with open(model["name"] + "_norm.bngl", "w") as f:
f.write(bnglString)
def getModelStructures(bngxml):
structures = readBNGXML.parseFullXML(bngxml)
return structures
