def generateGraph(self,ticket,bnglContents,graphtype): print ticket pointer = tempfile.mkstemp(suffix='.bngl',text=True) with open(pointer[1],'w' ) as f: f.write(bnglContents) #try: if graphtype in ['regulatory','contactmap']: consoleCommands.setBngExecutable(bngDistro) consoleCommands.generateGraph(pointer[1],graphtype) name = pointer[1].split('.')[0] with open('{0}_{1}.gml'.format(name,graphtype),'r') as f: graphContent = f.read() self.addToDict(ticket,graphContent) print 'success',ticket elif graphtype in ['sbgn_er']: consoleCommands.setBngExecutable(bngDistro) consoleCommands.generateGraph(pointer[1],'contactmap') name = pointer[1].split('.')[0] #with open('{0}_{1}.gml'.format(name,'contactmap'),'r') as f: # graphContent = f.read() graphContent = networkx.read_gml('{0}_{1}.gml'.format(name,'contactmap')) sbgn = libsbgn.createSBNG_ER_gml(graphContent) self.addToDict(ticket,sbgn) print 'success',ticket
import networkx import sys sys.path.insert(0, '../utils/') import consoleCommands import readBNGXML import libsbgn from datetime import datetime, timedelta def openGML(fileName, graphType): #consoleCommands.generateGraph(fileName,graphType) fileName = '.'.join( fileName.split('.')[:-1]) + '_{0}.gml'.format(graphType) model = networkx.read_gml(fileName) return model def readXML(fileName): #consoleCommands.bngl2xml(fileName) fileName = '.'.join(fileName.split('.')[:-1]) + '.xml' return readBNGXML.parseXML(fileName) if __name__ == "__main__": #molecules,reaction,parameters = readXML('BIOMD0000000019.xml.bngl') #print molecules contactMap = openGML('BIOMD0000000019.xml.bngl', 'contactmap') print '--', contactMap libsbgn.createSBNG_ER_gml(contactMap) #regulatory = openGML('BIOMD0000000019.xml.bngl','regulatory') #print model
@author: proto """ import networkx import sys sys.path.insert(0, '../utils/') import consoleCommands import readBNGXML import libsbgn from datetime import datetime,timedelta def openGML(fileName,graphType): #consoleCommands.generateGraph(fileName,graphType) fileName = '.'.join(fileName.split('.')[:-1]) + '_{0}.gml'.format(graphType) model = networkx.read_gml(fileName) return model def readXML(fileName): #consoleCommands.bngl2xml(fileName) fileName = '.'.join(fileName.split('.')[:-1]) + '.xml' return readBNGXML.parseXML(fileName) if __name__ == "__main__": #molecules,reaction,parameters = readXML('BIOMD0000000019.xml.bngl') #print molecules contactMap = openGML('BIOMD0000000019.xml.bngl','contactmap') print '--',contactMap libsbgn.createSBNG_ER_gml(contactMap) #regulatory = openGML('BIOMD0000000019.xml.bngl','regulatory') #print model