def test_parsing(self):
#reactionDefinitions, useID = libsbml2bngl.selectReactionDefinitions('BIOMD%010i.xml' % self.param)
#spEquivalence = detectCustomDefinitions(bioNumber)
print self.param
libsbml2bngl.analyzeFile('XMLExamples/curated/BIOMD%010i.xml' % self.param, 'reactionDefinitions/reactionDefinition7.json',
False, 'config/namingConventions.json',
'raw/output' + str(self.param) + '.bngl', speciesEquivalence=None,atomize=False,bioGrid=False)
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
ls2b.analyzeFile(options['inputFile'],options['conventionFile'],options['useId'],options['namingConventions'],
options['outputFile'],speciesEquivalence=options['userStructure'],
atomize=options['atomize'],bioGrid=False, pathwaycommons=options['pathwaycommons'])
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
ls2b.analyzeFile(options['inputFile'],options['conventionFile'],options['useId'],options['namingConventions'],
options['outputFile'],speciesEquivalence=options['userStructure'],
atomize=options['atomize'],bioGrid=options['biogrid'])
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
print options
ls2b.analyzeFile(options['inputFile'],options['conventionFile'],options['useId'],
options['outputFile'],speciesEquivalence=options['userStructure'],
atomize=options['atomize'],bioGrid=options['biogrid'])
def test_valid(self):
print self.param,
#deepreload.reload(libsbml2bngl)
libsbml2bngl.analyzeFile('{0}/{1}/{1}-sbml-l2v4.xml'.format(self.param[0],self.param[1]), '../reactionDefinitions/reactionDefinition7.json',
False, '../config/namingConventions.json',
'tmp/output' + str(self.param[1]) + '.bngl', speciesEquivalence=None,atomize=True,bioGrid=False)
settings = self.extractSimulationSettings('{0}/{1}/{1}-settings.txt'.format(self.param[0],self.param[1]))
bnglValues,atol = bnglExecution('output{0}'.format(self.param[1]),settings)
referenceValues = parseCSV('{0}/{1}/{1}-results.csv'.format(self.param[0],self.param[1]),settings['variables'])
print float(atol),((bnglValues - referenceValues)**2).mean()
self.assertAlmostEqual(((bnglValues - referenceValues)**2).mean(),0,delta=float(atol))
dirs = [ f for f in listdir('./tmp') if self.param[1] in f]
for element in dirs:
os.remove('./tmp/{0}'.format(element))
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'],
options['conventionFile'],
options['useId'],
options['namingConventions'],
options['outputFile'],
speciesEquivalence=options['userStructure'],
atomize=options['atomize'],
bioGrid=False,
pathwaycommons=options['pathwaycommons'],
ignore=options['ignore'],
noConversion=options['noConversion'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'],
namespace.bionetgen_analysis,
returnArray.database)
if namespace.annotation and returnArray:
with open(options['outputFile'] + '.yml', 'w') as f:
f.write(yaml.dump(returnArray.annotation,
default_flow_style=False))
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'], options['conventionFile'], options['useId'], options['namingConventions'],
options['outputFile'], speciesEquivalence=options['userStructure'],
atomize=options['atomize'], bioGrid=False, pathwaycommons=options['pathwaycommons'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'], namespace.bionetgen_analysis, returnArray.database)
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(options['inputFile'], options['conventionFile'], options['useId'], options['namingConventions'],
options['outputFile'], speciesEquivalence=options['userStructure'],
atomize=options['atomize'], bioGrid=False, pathwaycommons=options['pathwaycommons'], ignore=options['ignore'], noConversion = options['noConversion'])
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(options['outputFile'], namespace.bionetgen_analysis, returnArray.database)
if namespace.annotation and returnArray:
with open(options['outputFile'] + '.yml', 'w') as f:
f.write(yaml.dump(returnArray.annotation, default_flow_style=False))
def main():
parser = defineConsole()
namespace = parser.parse_args()
options = checkInput(namespace)
returnArray = ls2b.analyzeFile(
options["inputFile"],
options["conventionFile"],
options["useId"],
options["namingConventions"],
options["outputFile"],
speciesEquivalence=options["userStructure"],
atomize=options["atomize"],
bioGrid=False,
pathwaycommons=options["pathwaycommons"],
ignore=options["ignore"],
noConversion=options["noConversion"],
memoizedResolver=options["memoizedResolver"],
replaceLocParams=options["replaceLocParams"],
quietMode=options["quietMode"],
logLevel=options["logLevel"],
obs_map_file=options["obs_map_file"],
)
if namespace.bionetgen_analysis and returnArray:
ls2b.postAnalyzeFile(
options["outputFile"],
namespace.bionetgen_analysis,
returnArray.database,
replaceLocParams=options["replaceLocParams"],
)
if namespace.annotation and returnArray:
with open(options["outputFile"] + ".yml", "w") as f:
f.write(yaml.dump(returnArray.annotation,
default_flow_style=False))