class MDLR2MDL(object):
'''
given an mdlr definition this script will get a set of mdl files compatible with an nfsim bng-xml definition
'''
def __init__(self, configpath):
with open(configpath, 'r') as f:
self.config = yaml.load(f.read())
self.nfsim = NFSim(os.path.join(self.config['libpath'], 'libnfsim_c.so'))
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 tokenizeSeedElements(self, seed):
#extract species names
seedKeys = re.findall('concentration="[0-9a-zA-Z_]+" name="[_0-9a-zA-Z@:(~!),.]+"', seed)
seedKeys = [re.sub('concentration="([0-9a-zA-Z_]+)" name="([_0-9a-zA-Z@:(~!),.]+)"', '\g<2>;\g<1>', x) for x in seedKeys]
seedList = seed.split('</Species>')
seedList = [x.strip() for x in seedList if x != '']
seedList = [x + '</Species>' for x in seedList]
seedList = [re.sub('"S[0-9]+"', "S1", x) for x in seedList]
seedList = [re.sub('concentration="[0-9a-zA-Z_]+"', 'concentration="1"', x) for x in seedList]
seedList = ['<Model><ListOfSpecies>{0}</ListOfSpecies></Model>'.format(x) for x in seedList]
#seedDict = {x:y for x,y in zip(seedKeys,seedList)}
seedDict = {x.split(';')[0]:y for x, y in zip(seedKeys, seedList) if x.split(';')[1] != '0'}
#print '---', seedDict.keys()
return seedDict
def getNamesFromDefinitionString(self, defStr):
speciesNames = re.findall('[0-9a-zA-Z_]+\(',defStr)
return [x[:-1] for x in speciesNames]
def xml2HNautySpeciesDefinitions(self, inputMDLRFile):
"""
Temporary function for translating xml bng definitions to nautty species definition strings
it call the nfsim library to get the list of possible complexes in the system, however the function right now
returns the species in question + all molecule types (if we are sending a lone molecule tye as initialization
it still returns all molecule types), which means the list requires filterinng. and the filtering
is not pretty
How to solve: make it so that nfsim returns a more sensible complex list (filtering out unrelated molecule types) or
create a nauty label creation mechanism locally
"""
#get a bng-xml file
call([self.config['bionetgen'], '-xml', '-check', inputMDLRFile + '.bngl'])
#extract seed species defition
seed, rest = splitBNGXML.extractSeedBNG(inputMDLRFile + '.xml')
#store xml with non-seed sections and load up nfsim library
with open(namespace.input + '_total.xml', 'w') as f:
f.write(rest)
#load up nfsim library
self.nfsim.initNFsim(namespace.input + '_total.xml', 0)
# remove encapsulating tags
seed = seed[30:-30]
#get the seed species definitions as a list
seedDict = self.tokenizeSeedElements(seed)
nautyDict = {}
for seed in seedDict:
#initialize nfsim with each species definition and get back a dirty list where one of the entries is the one we want
#XXX: i think i've solved it on the nfsim side, double check
tmpList = self.getNautyString(seedDict[seed])
#and now filter it out...
#get species names from species definition string
speciesNames = self.getNamesFromDefinitionString(seed)
nautyDict[seed] = [x for x in tmpList if all(y in x for y in speciesNames)][0]
return nautyDict
def getNautyString(self, xmlSpeciesDefinition):
self.nfsim.resetSystem()
self.nfsim.initSystemXML(xmlSpeciesDefinition)
result = self.nfsim.querySystemStatus("complex")
return result
