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
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
