modelmage

204 """ 205 This class is the main interface for all the other classes. It is instantiated 206 by calling the module from the command line and by the web interface. The methods 207 provided by this class represent the main functionalities of the whole program. 208 """ 209 __masterModel = None 210 verbose = True 211

212 - def __init__(self, model=None, filename=None, verbose=False, output=''):

213 """ 214 The class can be initialized with various preset parameters. Depending on the 215 calling class. This way it can be used by the web interface as well as well as 216 from command line. 217 218 @type model: Model 219 @param model: a model that can be passed directly to the class and is set as 220 the master model 221 222 @type filename: str 223 @param filename: the filename of the file that was passed as a model. 224 225 @type verbose: bool 226 @param verbose: switch that decides if the output on the commandline is verbose 227 228 @type output: str 229 @param output: path and name of the output files 230 """ 231 232 if model: 233 self.setMasterModel(model) 234 self.filename = filename 235 self.output = output 236 self.verbose = verbose 237 self.master = '' 238 # indicate that the ReverseMacros and ReverseKineticsMacros 239 # are artifical created from the parameter of the option -k 240 self.buildReverseMacro = False 241 # define: key: function_6 value: Constant flux (irreversible) 242 # the content defined in getMasterSBMLFunctions(input) 243 # used in def assignFunctionNames() in generator.py 244 self.functionsIdName = {} 245 246 #setting the result folders, they are created in the generate method, if nessesary 247 self.currentResultsCopasi = os.path.join(self.output , ResultsCopasi) 248 self.currentResultsSBML = os.path.join(self.output , ResultsSBML)

249 250

251 - def setMasterModel(self, SBMLmodel=None, filename=None):

252 """ 253 This function sets the master model of the ModelMage instance. The model 254 can be given as an SBML file of a Model object. 255 256 @type SBMLmodel: Model 257 @param SBMLmodel: a model object that can be set as the master model 258 259 @type filename: str 260 @param filename: filename of the master model 261 """ 262 263 if filename: 264 inputPath = os.path.abspath(filename) 265 self.filename = inputPath 266 267 268 269 if SBMLmodel == None: 270 ################ 271 #read input file 272 input = filename 273 inputCPS = '' 274 if input[ - 4:] == ".cps": 275 self.master = input# for CCopasiDataModel.GLOBAL.loadModel 276 inputCPS = input 277 input = input[: - 4] + ".xml" 278 os.popen('CopasiSE %s -e %s' % (inputCPS, input)) 279 280 self.getMasterSBMLFunctions(input) 281 try: 282 ##This is a Workaround for incompatibilities with CellDesigner tags, they are removed before continuing 283 ##all existing files remain untouched 284 rootModel = model.Model() 285 inFile = unCellDesign.unCellDesign(input) 286 if inFile.isCellDesign(): 287 print 'Removing CellDesigner Tags...' 288 rootModel.readSBML(inFile.convert(), self.verbose) 289 else: 290 rootModel.readSBML(input, self.verbose) 291 292 except libSBMLError, e: 293 print "'%s' does not contain valid SBML. The following error occured:\n%s" % (input, e.type) 294 exit(0) 295 except Exception, e: 296 print e 297 exit(1) 298 self.__masterModel = rootModel 299 else: 300 self.__masterModel = model.Model() 301 self.__masterModel.readSBML(SBMLmodel)

302

303 - def getMasterSBMLFunctions(self, mastermodel):

304 ''' 305 This function produces the dictionary 306 {self.functionsIdName:{function_id : function_name}} 307 308 @type mastermodel: str 309 @param mastermodel: filename of the master model 310 ''' 311 312 mastermodel = os.path.abspath(mastermodel) 313 if os.path.exists(mastermodel): 314 pass 315 else: 316 print "%s does not exist. Exiting ...\n" % mastermodel 317 sys.exit(1) 318 319 inFile = unCellDesign.unCellDesign(mastermodel) 320 321 reader = lSBML.SBMLReader() 322 doc = reader.readSBMLFromString(inFile.convert()) 323 modelNew = doc.getModel() 324 325 functions = modelNew.getListOfFunctionDefinitions() 326 for function in functions: 327 #kineticLaw = lSBML.KineticLaw(function.getMath()) 328 # don't remove this output 329 #print "kinetic law formular: %s"%kineticLaw.getFormula() 330 331 # define: key: function_6 value: Constant flux (irreversible) 332 self.functionsIdName[function.getId()] = function.getName()

333 #print "function_id: %s\t name: %s"%(function.getId(), function.getName()) 334

335 - def getMasterModel(self):

336 """ 337 Returns the master model of the object. 338 """ 339 return self.__masterModel

340

341 - def getFilename(self):

342 """ 343 Returns the filename of the object. 344 """ 345 return self.filename

346

347 - def getMasterModelSpecies(self):

348 """ 349 Returns a list of species. 350 351 @rtype: list 352 @return: list of species 353 """ 354 return self.__masterModel.getModelElement('Species', ['Name', 'Id'])

355

356 - def getMasterModelReactions(self):

357 """ 358 Returns a list of reactions. 359 360 @rtype: list 361 @return: list of reactions 362 """ 363 return self.__masterModel.getModelElement('Reactions', ['Name', 'Id'])

364

365 - def transferData(self, expDataFiles):

366 """ 367 transfer the experimental data in the right place, so that the 368 process of parameter estimation can be properly executed 369 370 @return: list of experimental files 371 @rtype: list 372 """ 373 for file in expDataFiles: 374 file = str(file) 375 filename = os.path.split(file)[1] 376 datafilePath = os.path.split(file)[0] 377 filePath = os.path.split(self.filename)[0] 378 datafilePath = os.path.join(filePath,datafilePath) 379 datafilePath = os.path.normpath(datafilePath) 380 dataFile = os.path.join(datafilePath,filename) 381 target = os.path.join(self.currentResultsCopasi, filename) 382 if os.path.exists(dataFile): 383 shutil.copyfile(dataFile, target) 384 else: 385 print "Could not find data file for parameter estimation. Exiting ..." 386 exit(1)

387

388 - def generate(self, remove=None, kinetics=None, macros=None, useMacros=False, show=False):

389 """ 390 Generates the candidate models from the master model. 391 392 @type remove: str 393 @param remove: logical combination of elements that shall be removed 394 395 @type kinetics: str 396 @param kinetics: kinetics that shall be exchanged 397 398 @type macros: map 399 @param macros: contains the keys of candidate model name and values of remove combinations 400 401 @type useMacros: bool 402 @param useMacros: flag that tells if the user specified custom names for the models 403 404 @type show: bool 405 @param show: for -s --show option 406 """ 407 gen = GEN.Generator(self.__masterModel, self.functionsIdName, verbose=self.verbose) 408 409 # Generate alternatives: 410 REVERSEMACROS = [{}, {}] 411 ReverseMacros = {} 412 ReverseKineticMacros = {} 413 414 removeHandler = \ 415 PRE.removeHandler(self.__masterModel.getIdNameMap(), self.__masterModel.getNameIdMap()) 416 remove, ReverseMacros, macros = removeHandler.getTrueCombinations(remove, macros, useMacros) 417 418 #if remove or kinetics: 419 kineticHandler = PRE.kineticHandler() 420 if kinetics: 421 kinetics, ReverseKineticMacros = \ 422 kineticHandler.getKinetics(kinetics, self.__masterModel.getSbmlDocument(), macros) 423 424 # build the dictionary for reactions and their corresponding assigned models 425 REVERSEMACROS = [ReverseMacros, ReverseKineticMacros] 426 if kinetics: 427 try: 428 partOfModel = kineticHandler.checkPartOfModel(self.__masterModel.getSbmlDocument().getModel(), kinetics.keys()) 429 except InputError, e: 430 partOfModel = 0 431 print e.message 432 print "Continue with Mass Action Kinetics..." 433 if partOfModel: 434 pass 435 else: 436 print """\nGiven reaction ids \"%s\" are not part of the model. 437 These ids will not be used as kinetic alternatives.""" % kineticHandler.getNonModelIds() 438 for id in kineticHandler.getNonModelIds(): 439 kinetics.pop(id) 440 if remove: 441 newKineticsDocuments, nameKineticNameMap, modelFunctionsIdName, idNameReactions = \ 442 gen.generate(remove, kinetics, REVERSEMACROS, self.verbose) 443 gen.printReactionsSpecies(remove) 444 else: 445 newKineticsDocuments, nameKineticNameMap, modelFunctionsIdName, idNameReactions = \ 446 gen.generate([], kinetics, REVERSEMACROS, self.verbose) 447 gen.printReactionsSpecies() 448 449 #exit if show option was given 450 if show: 451 print "\n\n" 452 sys.exit(0) 453 454 # outputModels = newKineticsDocuments 455 self.graphHistory = gen.getGraphHistory() 456 idNameMap = gen.getModel().getIdNameMap() 457 458 459 if not os.path.exists(self.output): 460 try: 461 os.mkdir(self.output) 462 except: 463 print "Could not create output directory %s. Exiting ..." % self.output 464 sys.exit(1) 465 466 if not os.path.exists(self.currentResultsSBML): 467 try: 468 os.mkdir(self.currentResultsSBML) 469 except: 470 print "Could not create SBML output directory. Exiting ..." 471 sys.exit(1) 472 473 #print '\n\nWriting SBML files: <p>' 474 createdSBML = [] 475 filelist = [] 476 477 # usedName for the case when there are more than one keys in ReverseMacros 478 # having the same value, which will be defined as the copasi and sbml filenames 479 usedName = {} 480 print "\n", 481 for key, newDocument in newKineticsDocuments.items(): 482 for i, doc in enumerate(newDocument): 483 #use the modelname defined in initial file 484 name = ReverseMacros[key] 485 sbmlFileName = ReverseMacros[key] 486 usedName[name] = 1 487 if i > 0: 488 newsbmlFileName = "%sK%s" % (sbmlFileName, i) 489 modelFunctionsIdName[newsbmlFileName] = modelFunctionsIdName[sbmlFileName] 490 sbmlFileName = newsbmlFileName 491 492 # remove ':' from filename for window system 493 if sbmlFileName.rfind(':') != -1: 494 sbmlFileName = sbmlFileName.replace(':','_') 495 filelist.append(sbmlFileName) 496 doc.writeSBML(os.path.join(self.currentResultsSBML, sbmlFileName)) 497 createdSBML.append(os.path.join(self.currentResultsSBML, sbmlFileName) + ".xml") 498 print "\tgenerating %s.xml" % (os.path.split(sbmlFileName)[-1]) 499 #self.getCandidateSBMLFunctions(sbmlFileName) 500 print '\nSBML files generated.\n' 501 502 # define map with key reaction-id and reaction-name 503 # key: reaction_1 value: v1 504 self.idNameReactions = idNameReactions 505 self.filelist = filelist 506 507 #create copasi files: 508 if not os.path.exists(self.currentResultsCopasi): 509 try: 510 os.mkdir(self.currentResultsCopasi) 511 except: 512 print "Could not create Copasi output directory. Exiting ..." 513 sys.exit(1) 514 515 createdCPS = [] 516 if os.path.exists(self.currentResultsSBML): 517 #print '\nWriting Copasi files:' 518 if filelist: 519 for f in filelist: 520 sfile = os.path.join(self.currentResultsSBML, f) + '.xml' 521 cfile = os.path.join(self.currentResultsCopasi, f) + '.cps' 522 if os.path.exists(sfile): 523 im = "-i %s" % sfile 524 exp = "-s %s" % cfile 525 print "\tgenerating %s"%(os.path.split(cfile)[-1]) 526 os.popen("CopasiSE %s %s" % (im, exp)) 527 createdCPS.append(cfile) 528 else: 529 print "No such file or directory: %s" % sfile 530 print '\nCopasi files generated.\n' 531 else: 532 print 'No SBML files in directory %s. \ 533 CopasiFile cannot be generated. Exiting ...\n' % self.currentResultsSBML 534 sys.exit(1) 535 else: 536 print 'Directory %s does not exist. \ 537 CopasiFile cannot be generated. Exiting ...\n' % self.currentResultsSBML 538 sys.exit(1) 539 540 if self.verbose: 541 print 'Specifying tasks...' 542 543 if self.filename[ - 4:] == ".xml": 544 inputCPS = None 545 self.Update_tasks_cps(modelFunctionsIdName, nameKineticNameMap, ReverseMacros, idNameMap, inputCPS) 546 547 if self.filename[ - 4:] == ".cps": 548 inputCPS = self.filename 549 rootFile = GEN.CpsHandler(inputCPS, self.graphHistory) 550 expDataFiles = rootFile.getExperimentalDataFiles() 551 self.transferData(expDataFiles) 552 553 self.Update_tasks_cps(modelFunctionsIdName, nameKineticNameMap, ReverseMacros, idNameMap, inputCPS)

554 555 ##### end of programm ##### 556 557

558 - def Update_tasks_cps(self, modelFunctionsIdName, nameKineticNameMap, ReverseMacros, idNameMap, inputCPS):

559 ''' 560 Updates tasks in cps files, so they can be used for parameter estimation. 561 562 @rtype: None 563 @return: None 564 ''' 565 newFileList = [] 566 for file in self.filelist: 567 newFileList.append(os.path.split(file)[-1]) 568 # 569 self.newFileList = newFileList 570 571 print "Updating tasks for generated Copasi candidate models ... \n" 572 for file in [x for x in glob.glob(os.path.join(self.currentResultsCopasi,"*.cps")) \ 573 if os.path.split(x)[ - 1][: - 4] in self.newFileList]: 574 575 fileSym = os.path.split(file)[-1][:-4] 576 readyForAssignFunc = False 577 578 # if control by the ini file 579 if (fileSym in modelFunctionsIdName.keys()): 580 # define key: v10 value: function_7 581 functionReactionMap = self.getFunction_Id_Name_XML(fileSym, self.idNameReactions) 582 functionsIdName = modelFunctionsIdName[fileSym] 583 # define: key: v10 value: Mass action 584 newKineticNameMap = {} 585 # define: key: v10:ca3 value: Mass action 586 for key, value in nameKineticNameMap.items(): 587 newKey = key.split(':')[0] 588 symbol = key.split(':')[1] 589 if symbol == fileSym: 590 newKineticNameMap[newKey] = value 591 592 readyForAssignFunc = True 593 594 #indicate that there is no ini file being used 595 else: 596 # define key: v10 value: function_7 597 functionReactionMap = self.getFunction_Id_Name_XML(fileSym, self.idNameReactions) 598 functionsIdName = {} 599 # want to get key = reaction_7reaction_1 or s4r3 600 if len(modelFunctionsIdName) > 1: 601 key = keypattern[0] 602 print modelFunctionsIdName 603 functionsIdName = modelFunctionsIdName[key] 604 # more than one candidate model has been generated 605 else: 606 for key, value in modelFunctionsIdName.items(): 607 for ke, va in value.items(): 608 functionsIdName[ke] = va 609 610 newKineticNameMap = nameKineticNameMap 611 readyForAssignFunc = True 612 613 cpsFile = GEN.CpsHandler(file, self.graphHistory, idNameMap) 614 if readyForAssignFunc: 615 cpsFile.assignFunctionNames(functionReactionMap, functionsIdName, fileSym, newKineticNameMap) 616 try: 617 if self.verbose: 618 print "\nFile: %s:" % file 619 if inputCPS: 620 removedFitItems = cpsFile.importTask(inputCPS, 'parameterFitting') 621 if self.verbose: 622 for item in removedFitItems: 623 print "Removed fititem reaction: %s parameter: %s" % item 624 625 except IOError, e: 626 print "\nError:\nFile '{rootModel}.cps' not found, you need to create that \ 627 file (with CopasiUI) and specify estimation parameters in this file." 628 exit(1) 629 try: 630 written = cpsFile.writeCPS(file) 631 if not written: 632 exit(1) 633 except Exception, e: 634 print '\nError:\n%s' % e 635 exit(1)

636 637

638 - def getFunction_Id_Name_XML(self, modelName, idNameReactions):

639 """ 640 This function constructs a dictionary with the keys of reaction_id 641 and the values of corresponding function_id 642 643 @type modelName: str 644 @param modelName: filename of the master model 645 646 @type idNameReactions: dictionary 647 @param idNameReactions: {reaction_id : reaction_name} 648 649 @return: a map of { functionReactionMap:{reaction_id : function_id} }used by def assignFunctionNames() in generator.py 650 """ 651 652 modelPath = os.path.join(os.path.abspath('.'),self.currentResultsSBML,modelName) + '.xml' 653 #print "\nmodelPath: %s"%modelPath 654 if os.path.exists(modelPath): 655 pass 656 else: 657 print "%s does not exist. Exiting ...\n" % modelPath 658 sys.exit(1) 659 660 # reading the SBML file 661 inFile = unCellDesign.unCellDesign(modelPath) 662 reader = lSBML.SBMLReader() 663 doc = reader.readSBMLFromString(inFile.convert()) 664 modelNew = doc.getModel() 665 # functions = modelNew.getListOfFunctionDefinitions() 666 667 # check the defined kinetic laws 668 #for function in functions: 669 #kineticLaw = lSBML.KineticLaw(function.getMath()) 670 #print "kineticLaw: %s"%kineticLaw.getFormula() 671 672 functionReactionMap = {} 673 reactions = modelNew.getListOfReactions() 674 675 for reaction in reactions: 676 kine = reaction.getKineticLaw().getFormula() 677 #print "reaction: %s\tkine: %s"%(reaction.getId(), kine) 678 if '*' in kine: 679 withoutCom = kine.split('*')[1] 680 fun = withoutCom.split('(')[0] 681 else: 682 fun = kine.split('(')[0] 683 vId = idNameReactions[reaction.getId()] 684 685 # sometimes there is no defined id for reaction 686 if vId == '': 687 pseName = str(reaction.getId()) 688 functionReactionMap[pseName] = fun.strip(" ") 689 else: 690 functionReactionMap[vId] = fun.strip(" ") 691 692 return functionReactionMap

693 694 # for control purpose 695 #

696 - def getCandidateSBMLFunctions(self, candidateName):

697 ''' 698 This function produces the dictionary 699 {self.functionsIdName:{function_id : function_name}} 700 701 @type candidateName: str 702 @param candidateName: filename of the model 703 ''' 704 705 path = '/result/ResultSBMLFiles/' 706 candidateName = os.path.split(candidateName)[ - 1] 707 modelPath = os.path.abspath('.') + path + candidateName + '.xml' 708 #modelPath = mastermodel + '.xml' 709 #print "\nMaster model: %s\n\n"%modelPath 710 if os.path.exists(modelPath): 711 pass 712 else: 713 print "%s does not exist. Exiting ...\n"%modelPath 714 sys.exit(1) 715 716 inFile = unCellDesign.unCellDesign(modelPath) 717 718 reader = lSBML.SBMLReader() 719 doc = reader.readSBMLFromString(inFile.convert()) 720 modelNew = doc.getModel() 721 722 functions = modelNew.getListOfFunctionDefinitions() 723 for function in functions: 724 kineticLaw = lSBML.KineticLaw(function.getMath())

725 # print "kinetic law formula: %s" % kineticLaw.getFormula() # don't remove this output 726 727 # define: key: function_6 value: Constant flux (irreversible) 728 #self.functionsIdName[function.getId()] = function.getName() 729 # print "function_id: %s\t name: %s"%(function.getId(), function.getName()) 730 731

732 - def estimateParameters(self):

733 """ 734 This method starts a parameter estimation for all created output files. 735 """ 736 for file in [x for x in glob.glob('%s/*.cps' % self.currentResultsCopasi)\ 737 if os.path.split(x)[ - 1][: - 4] in self.newFileList]: 738 print 'Estimating parameters for %s ...' % file , 739 sys.stdout.flush() 740 try: 741 if self.verbose: 742 os.popen('CopasiSE %s -s %s --verbose' % (file, file)) 743 else: 744 #print('CopasiSE %s -s %s \n' % (file, file)) 745 os.popen('CopasiSE %s -s %s' % (file, file)) 746 ## after execute this command copasi will create the parameter estimation task log file 747 print 'Done.\n\tResults written to %s' % file.split('.')[0] + '_est.txt' 748 except Exception, e: 749 print '\nError:\nCopasi was not able to estimate.\nMessage: %s' % e.message 750 print "\n"

751

752 - def discriminate(self):

753 """ 754 This method returns a ranking of the estimated models that is produced by 755 L{Discriminator} 756 """ 757 if os.path.exists(self.currentResultsCopasi): 758 d = DIS.Discriminator(self.currentResultsCopasi) 759 else: 760 print "Directory %s does not exist. Cannot parse parameter estimation results. Exiting ..." % os.path.abspath(self.currentResultsCopasi) 761 sys.exit(1) 762 #return d.getRanking() 763 print d.getRanking()

Source Code for Module modelmage