biana.BianaParser.psi

1 """ 2 File : psi_MiXMLParser.py 3 Author : Javier Garcia & Emre Guney 4 Creation : December 2007 5 Contents : 6 - Psi_MiXMLParser object to parse an XML file in PSI-MI (PSI molecular interaction format) 7 - Psi_MiEntry object which corresponds to the "entry" in the file (container for interactors & interactions) 8 - Psi_MiInteractor object 9 - Psi_MiInteraction object 10 - Psi_MiParticipant object 11 - Psi_MiNames object 12 - Psi_MiXref object 13 - DBReference object 14 - Psi_MiHandler object (Content Handler for XML parsing with SAX) 15 16 Called from : psi_MiFormattedDB2piana.py 17 18 ======================================================================================================= 19 20 Generic parser aiming to read data available in PSI-MI XML format in various databases 21 22 """ 23 24 #import xml.dom.minidom 25 from xml.sax import saxutils, handler, make_parser 26 27 #import time 28 #TIME_CHECK = 0 # time.clock() 29 30 """ 31 ======================================================================================================= 32 Psi_MiXMLParser OBJECT 33 """ 34

35 -class Psi_MiXMLParser:

36 """ 37 Class for parsing individual XML files obeying PSI-MI standarts 38 """ 39

40 - def __init__(self, flagVerbose=False): #, fileName=None, listEntry=None):

41 self.fileName = None 42 self.file = None 43 self.listEntry = [] 44 self.handler = Psi_MiHandler(flagVerbose) 45 self.saxParser = make_parser() 46 self.saxParser.setContentHandler(self.handler) 47 return

48

49 - def __del__(self):

50 if self.file is not None and not self.file.closed: 51 self.file.close() 52 return

53

54 - def __str__(self):

55 return ""

56

57 - def parseFile(self, fileName=None):

58 self.__init__() # first reset old contents 59 if fileName is not None: 60 self.fileName = fileName 61 self.file = open(fileName) 62 self.saxParser.parse(self.fileName) 63 #objPsi_MiEntry = self._parseEntry(node) 64 #self.addEntry(objPsi_MiEntry) 65 self.listEntry = self.handler.listEntry 66 if not self.file.closed: 67 self.file.close() 68 return

69

70 - def addEntry(self, objPsi_MiEntry):

71 self.listEntry.append(objPsi_MiEntry) 72 return

73

74 - def getEntries(self):

75 return self.listEntry

76 77 """ 78 ======================================================================================================= 79 Psi_MiEntry OBJECT 80 """

81 -class Psi_MiHandler(handler.ContentHandler):

82 """ 83 Class to handle content in PSI-MI XML files 84 """

85 - def __init__(self, flagVerbose):

86 handler.ContentHandler.__init__(self) 87 self.listTagStack = [] 88 self.listObjectStack = [] 89 #self.tagCurrentParent = None # either: experiment, interaction, interactor, ?? participant 90 #self.objPsi_MiCurrent = None 91 self.strCurrent = None 92 self.tagCurrent = None 93 self.strAttributeCurrent = None 94 self.listEntry = [] 95 self.flagVerbose = flagVerbose 96 return

97

98 - def _printObjectStack(self):

99 print self.listObjectStack 100 return

101

102 - def _getAttribute(self, attrs, nameAttribute, flagReportInExistance=False):

103 strAttribute = None 104 for (name, value) in attrs.items(): 105 if name == nameAttribute: 106 strAttribute = saxutils.escape(value) 107 if strAttribute is None and flagReportInExistance: 108 if self.flagVerbose: 109 print "Warning: Attribute not found - %s", nameAttribute 110 return strAttribute

111 112 # ContentHandler methods

113 - def startDocument(self):

114 return

115

116 - def startElement(self, name, attrs):

117 ##print name 118 if name == Psi_MiEntry.PSI_MI_TAG_ENTRY: 119 self.listObjectStack.append(Psi_MiEntry()) 120 elif name == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 121 id = self._getAttribute(attrs, Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_ATTRIBUTE_ID, True) 122 self.listObjectStack.append(Psi_MiExperiment(id)) 123 elif name == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 124 id = self._getAttribute(attrs, Psi_MiInteractor.PSI_MI_TAG_INTERACTOR_ATTRIBUTE_ID, True) 125 #print id, 126 self.listObjectStack.append(Psi_MiInteractor(id)) 127 elif name == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 128 id = self._getAttribute(attrs, Psi_MiInteraction.PSI_MI_TAG_INTERACTION_ATTRIBUTE_ID, True) 129 self.listObjectStack.append(Psi_MiInteraction(id)) 130 elif name == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT: 131 if self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_PARTICIPANT_LIST: 132 id = self._getAttribute(attrs, Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT_ATTRIBUTE_ID, True) 133 self.listObjectStack.append(Psi_MiParticipant(id)) 134 elif name == Psi_MiNames.PSI_MI_TAG_NAMES: 135 # inserting many unnecessary objects (names inside which are not used but the other way is checking all coupled tag relationships) 136 self.listObjectStack.append(Psi_MiNames()) 137 elif name == Psi_MiNames.PSI_MI_TAG_ALIAS: 138 if self.listTagStack[-1] == Psi_MiNames.PSI_MI_TAG_NAMES: 139 self.strAttributeCurrent = self._getAttribute(attrs, Psi_MiNames.PSI_MI_TAG_ALIAS_ATTRIBUTE_TYPE) 140 elif name == Psi_MiXRef.PSI_MI_TAG_XREF: 141 self.listObjectStack.append(Psi_MiXRef()) 142 elif name == Psi_MiXRef.PSI_MI_TAG_REF_PRIMARY: 143 #if self.listTagStack[-1] == Psi_MiXRef.PSI_MI_TAG_XREF: 144 objPsi_MiXRef = self.listObjectStack[-1] 145 db = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_DB, True) 146 id = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_ID, True) 147 type = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_TYPE) 148 secondary = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_SECONDARY) 149 objPsi_MiXRef.refPrimary = DBReference(db, id, type, secondary) 150 elif name == Psi_MiXRef.PSI_MI_TAG_REF_SECONDARY: 151 objPsi_MiXRef = self.listObjectStack[-1] 152 db = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_DB) 153 id = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_ID) 154 type = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_TYPE) 155 secondary = self._getAttribute(attrs, Psi_MiXRef.PSI_MI_TAG_REF_ATTRIBUTE_SECONDARY) 156 objPsi_MiXRef.listRefSecondary.append(DBReference(db, id, type, secondary)) 157 elif name == Psi_MiInteractor.PSI_MI_TAG_ORGANISM: 158 if self.listTagStack[-1] == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 159 objPsi_MiInteractor = self.listObjectStack[-1] 160 objPsi_MiInteractor.taxId = self._getAttribute(attrs, Psi_MiInteractor.PSI_MI_TAG_ORGANISM_ATTRIBUTE_TAX_ID, True) 161 #self._printObjectStack() 162 self.listTagStack.append(name) 163 self.tagCurrent = name # to be able to remember the last tag inserted into stack and combine strings splitted inside the same tag by characters function 164 return

165

166 - def endElement(self, name):

167 tagPrevious = self.listTagStack.pop() 168 if name != tagPrevious: 169 print "Warning: Tag inconsistency in stack", name 170 if name == Psi_MiEntry.PSI_MI_TAG_ENTRY: 171 objPsi_MiEntry = self.listObjectStack.pop() 172 self.listEntry.append(objPsi_MiEntry) 173 elif name == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 174 if self.listTagStack[-1] == Psi_MiEntry.PSI_MI_TAG_INTERACTOR_LIST and self.listTagStack[-2] == Psi_MiEntry.PSI_MI_TAG_ENTRY: 175 objPsi_MiInteractor = self.listObjectStack.pop() 176 objPsi_MiEntry = self.listObjectStack[-1] 177 objPsi_MiEntry.addInteractor(objPsi_MiInteractor) 178 elif self.listTagStack[-1] == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT and self.listTagStack[-2] == Psi_MiInteraction.PSI_MI_TAG_PARTICIPANT_LIST and self.listTagStack[-3] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 179 objPsi_MiInteractor = self.listObjectStack.pop() 180 objPsi_MiParticipant = self.listObjectStack[-1] 181 #objPsi_MiInteraction = self.listObjectStack[-2] 182 objPsi_MiEntry = self.listObjectStack[-3] 183 objPsi_MiEntry.addInteractor(objPsi_MiInteractor) 184 objPsi_MiParticipant.interactorId = objPsi_MiInteractor.id 185 elif name == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 186 if self.listTagStack[-1] == Psi_MiEntry.PSI_MI_TAG_EXPERIMENT_LIST and self.listTagStack[-2] == Psi_MiEntry.PSI_MI_TAG_ENTRY: 187 objPsi_MiExperiment = self.listObjectStack.pop() 188 objPsi_MiEntry = self.listObjectStack[-1] 189 objPsi_MiEntry.addExperiment(objPsi_MiExperiment) 190 elif self.listTagStack[-1] == Psi_MiEntry.PSI_MI_TAG_EXPERIMENT_LIST and self.listTagStack[-2] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 191 objPsi_MiExperiment = self.listObjectStack.pop() 192 objPsi_MiInteraction = self.listObjectStack[-1] 193 objPsi_MiEntry = self.listObjectStack[-2] 194 objPsi_MiEntry.addExperiment(objPsi_MiExperiment) 195 objPsi_MiInteraction.listExperimentId.append(objPsi_MiExperiment.id) 196 elif name == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 197 objPsi_MiInteraction = self.listObjectStack.pop() 198 objPsi_MiEntry = self.listObjectStack[-1] 199 objPsi_MiEntry.addInteraction(objPsi_MiInteraction) 200 elif name == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT: 201 if self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_PARTICIPANT_LIST: 202 objPsi_MiParticipant = self.listObjectStack.pop() 203 objPsi_MiInteraction = self.listObjectStack[-1] 204 objPsi_MiInteraction.addParticipant(objPsi_MiParticipant) 205 elif name == Psi_MiNames.PSI_MI_TAG_NAMES: 206 #if isinstance(objPsi_MiCurrent, Psi_MiInteractor): 207 objPsi_MiNames = self.listObjectStack.pop() 208 if self.listTagStack[-1] == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 209 objPsi_MiInteractor = self.listObjectStack[-1] 210 objPsi_MiInteractor.name = objPsi_MiNames 211 #print objPsi_MiNames.name, objPsi_MiNames.label 212 elif self.listTagStack[-1] == Psi_MiInteractor.PSI_MI_TAG_TYPE: 213 objPsi_MiInteractor = self.listObjectStack[-1] 214 objPsi_MiInteractor.type = objPsi_MiNames 215 #print objPsi_MiNames.name, objPsi_MiNames.label 216 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 217 objPsi_MiExperiment = self.listObjectStack[-1] 218 objPsi_MiExperiment.description = objPsi_MiNames 219 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_INTERACTION_DETECTION_METHOD and self.listTagStack[-2] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 220 objPsi_MiExperiment = self.listObjectStack[-1] 221 objPsi_MiExperiment.nameMethodInteraction = objPsi_MiNames 222 elif self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 223 objPsi_MiInteraction = self.listObjectStack[-1] 224 objPsi_MiInteraction.name = objPsi_MiNames 225 elif self.listTagStack[-1] == Psi_MiParticipant.PSI_MI_TAG_BIOLOGICAL_ROLE and self.listTagStack[-2] == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT: 226 objPsi_MiParticipant = self.listObjectStack[-1] 227 objPsi_MiParticipant.nameRoleBiological = objPsi_MiNames 228 elif self.listTagStack[-1] == Psi_MiParticipant.PSI_MI_TAG_EXPERIMENTAL_ROLE and self.listTagStack[-2] == Psi_MiParticipant.PSI_MI_TAG_EXPERIMENTAL_ROLE_LIST and self.listTagStack[-3] == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT: 229 objPsi_MiParticipant = self.listObjectStack[-1] 230 objPsi_MiParticipant.listNameRoleExperimental.append(objPsi_MiNames) 231 elif name == Psi_MiNames.PSI_MI_TAG_NAME: 232 if self.listTagStack[-1] == Psi_MiNames.PSI_MI_TAG_NAMES: 233 objPsi_MiNames = self.listObjectStack[-1] 234 objPsi_MiNames.name = self.strCurrent 235 elif name == Psi_MiNames.PSI_MI_TAG_LABEL: 236 if self.listTagStack[-1] == Psi_MiNames.PSI_MI_TAG_NAMES: 237 objPsi_MiNames = self.listObjectStack[-1] 238 objPsi_MiNames.label = self.strCurrent 239 elif name == Psi_MiNames.PSI_MI_TAG_ALIAS: 240 if self.listTagStack[-1] == Psi_MiNames.PSI_MI_TAG_NAMES: 241 objPsi_MiNames = self.listObjectStack[-1] 242 objPsi_MiNames.listAlias.append((self.strAttributeCurrent, self.strCurrent)) 243 elif name == Psi_MiXRef.PSI_MI_TAG_XREF: 244 objPsi_MiXRef = self.listObjectStack.pop() 245 if self.listTagStack[-1] == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 246 objPsi_MiInteractor = self.listObjectStack[-1] 247 objPsi_MiInteractor.xRef = objPsi_MiXRef 248 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_BIB_REF and self.listTagStack[-2] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 249 objPsi_MiExperiment = self.listObjectStack[-1] 250 objPsi_MiExperiment.xRefBib = objPsi_MiXRef 251 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 252 objPsi_MiExperiment = self.listObjectStack[-1] 253 objPsi_MiExperiment.xRef = objPsi_MiXRef 254 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_INTERACTION_DETECTION_METHOD and self.listTagStack[-2] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 255 objPsi_MiExperiment = self.listObjectStack[-1] 256 objPsi_MiExperiment.xRefMethodInteraction = objPsi_MiXRef 257 elif self.listTagStack[-1] == Psi_MiExperiment.PSI_MI_TAG_PARTICIPANT_IDENTIFICATION_METHOD and self.listTagStack[-2] == Psi_MiExperiment.PSI_MI_TAG_EXPERIMENT_DESCRIPTION: 258 objPsi_MiExperiment = self.listObjectStack[-1] 259 objPsi_MiExperiment.xRefMethodParticipant = objPsi_MiXRef 260 elif self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 261 objPsi_MiInteraction = self.listObjectStack[-1] 262 objPsi_MiInteraction.xRef = objPsi_MiXRef 263 elif self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_TYPE: 264 objPsi_MiInteraction = self.listObjectStack[-1] 265 objPsi_MiInteraction.type = objPsi_MiXRef 266 elif name == Psi_MiInteractor.PSI_MI_TAG_SEQUENCE: 267 if self.listTagStack[-1] == Psi_MiInteractor.PSI_MI_TAG_INTERACTOR: 268 objPsi_MiInteractor = self.listObjectStack[-1] 269 objPsi_MiInteractor.sequence = self.strCurrent 270 elif name == Psi_MiInteraction.PSI_MI_TAG_EXPERIMENT_REFERENCE: 271 if self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_EXPERIMENT_LIST and self.listTagStack[-2] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 272 objPsi_MiInteraction = self.listObjectStack[-1] 273 objPsi_MiInteraction.listExperimentId.append(self.strCurrent) 274 elif name == Psi_MiInteraction.PSI_MI_TAG_NEGATIVE: 275 if self.listTagStack[-1] == Psi_MiInteraction.PSI_MI_TAG_INTERACTION: 276 objPsi_MiInteraction = self.listObjectStack[-1] 277 objPsi_MiInteraction.negative = True 278 elif name == Psi_MiParticipant.PSI_MI_TAG_INTERACTOR_REFERENCE: 279 if self.listTagStack[-1] == Psi_MiParticipant.PSI_MI_TAG_PARTICIPANT: 280 objPsi_MiParticipant = self.listObjectStack[-1] 281 objPsi_MiParticipant.interactorId = self.strCurrent 282 self.strCurrent = None 283 #self._printObjectStack() 284 return

285

286 - def characters(self, content):

287 #if content != "" or content != " " or content != "\t": 288 # print "char:", saxutils.escape(content) 289 if self.tagCurrent == self.listTagStack[-1]: 290 #if content != "\n" and content != "\t" and content != " " and content != " ": 291 # self.strCurrent += content 292 if content.lstrip() != "": 293 if self.strCurrent is None: 294 self.strCurrent = content.lstrip() 295 else: 296 self.strCurrent += content.lstrip() 297 else: 298 #self.strCurrent = content 299 if content.lstrip() != "": 300 self.strCurrent = content.lstrip() 301 return

302

303 - def ignorableWhitespace(self, content):

304 #print content 305 return

306

307 - def processingInstruction(self, target, data):

308 #self._out.write('<?%s %s?>' % (target, data)) 309 print "Skipping Processing Instruction: %s %s" % (target, data) 310 return

311

312 - def skippedEntity(self, name):

313 print "Skipping Entity: %s" % name 314 return

315 316 317 """ 318 ======================================================================================================= 319 Psi_MiEntry OBJECT 320 """

321 -class Psi_MiEntry:

322 """ 323 Class representing an entry 324 """ 325 PSI_MI_TAG_ENTRY = "entry" 326 PSI_MI_TAG_EXPERIMENT_LIST = "experimentList" 327 PSI_MI_TAG_INTERACTOR_LIST = "interactorList" 328 PSI_MI_TAG_INTERACTION_LIST = "interactionList" 329

330 - def __init__(self, dictExperiment=None, dictInteractor=None, dictInteraction=None):

331 if dictExperiment is None: 332 self.dictExperiment = {} 333 else: 334 self.dictExperiment = dictExperiment 335 if dictInteractor is None: 336 self.dictInteractor = {} 337 else: 338 self.dictInteractor = dictInteractor 339 if dictInteraction is None: 340 self.dictInteraction = {} 341 else: 342 self.dictInteraction = dictInteraction 343 return

344

345 - def __del__(self):

346 return

347

348 - def __str__(self):

349 return "%s" % [k for k in self.dictInteractor.iterkeys()]

350

351 - def addExperiment(self, objPsi_MiExperiment):

352 self.dictExperiment[objPsi_MiExperiment.id] = objPsi_MiExperiment 353 return True

354

355 - def addInteractor(self, objPsi_MiInteractor):

356 self.dictInteractor[objPsi_MiInteractor.id] = objPsi_MiInteractor 357 return True

358

359 - def addInteraction(self, objPsi_MiInteraction):

360 self.dictInteraction[objPsi_MiInteraction.id] = objPsi_MiInteraction 361 return True

362

363 - def getExperiments(self):

364 return self.dictExperiment

365

366 - def getInteractors(self):

367 return self.dictInteractor

368

369 - def getInteractions(self):

370 return self.dictInteraction

371 372 """ 373 ======================================================================================================= 374 Psi_MiExperiment OBJECT 375 """

376 -class Psi_MiExperiment:

377 """ 378 Class representing an interactor 379 """ 380 381 PSI_MI_TAG_EXPERIMENT_DESCRIPTION = "experimentDescription" 382 PSI_MI_TAG_EXPERIMENT_ATTRIBUTE_ID = "id" 383 PSI_MI_TAG_BIB_REF = "bibref" 384 PSI_MI_TAG_INTERACTION_DETECTION_METHOD = "interactionDetectionMethod" 385 PSI_MI_TAG_PARTICIPANT_IDENTIFICATION_METHOD = "participantIdentificationMethod" 386

387 - def __init__(self, id=None, objPsi_MiNames=None, objPsi_MiXRefBib=None, objPsi_MiXRef=None, objPsi_MiXRefMethodInteraction=None, objPsi_MiXRefMethodParticipant=None, objPsi_MiNamesType=None):

388 """ 389 id: in PSI_MI_TAG_EXPERIMENT_ATTRIBUTE_ID 390 objPsi_MiXRefBib: inside PSI_MI_TAG_BIBREF inside PSI_MI_TAG_XREF 391 objPsi_MiXRef: inside PSI_MI_TAG_XREF 392 objPsi_MiXRefMethodInteraction: inside PSI_MI_TAG_INTERACTION_DETECTION_METHOD 393 objPsi_MiXRefMethodParticipant: inside PSI_MI_TAG_PARTICIPANT_IDENTIFICATION_METHOD 394 395 """ 396 self.id = id # An integer represented as string 397 self.description = objPsi_MiNames 398 self.xRefBib = objPsi_MiXRefBib 399 self.xRef = objPsi_MiXRef 400 self.xRefMethodInteraction = objPsi_MiXRefMethodInteraction # Interaction method as xRef 401 self.xRefMethodParticipant = objPsi_MiXRefMethodParticipant 402 self.nameMethodInteraction = objPsi_MiNamesType # Interaction method as name 403 return

404

405 - def __del__(self):

406 return

407

408 - def __str__(self):

409 return "{%s: %s, %s, %s, %s}" % (self.id, self.xRefBib, self.xRef, self.xRefMethodInteraction, self.xRefMethodParticipant)

410 411 412 """ 413 ======================================================================================================= 414 Psi_MiInteractor OBJECT 415 """

416 -class Psi_MiInteractor:

417 """ 418 Class representing an interactor 419 """ 420 421 PSI_MI_TAG_INTERACTOR = "interactor" 422 PSI_MI_TAG_INTERACTOR_ATTRIBUTE_ID = "id" 423 PSI_MI_TAG_TYPE = "interactorType" 424 PSI_MI_TAG_ORGANISM = "organism" 425 PSI_MI_TAG_ORGANISM_ATTRIBUTE_TAX_ID = "ncbiTaxId" 426 PSI_MI_TAG_SEQUENCE = "sequence" 427

428 - def __init__(self, id=None, objPsi_MiNames=None, objPsi_MiXRef=None, objPsi_MiNamesType=None, taxId=None, sequence=None): #, label=None, name=None, listAlias=None):

429 """ 430 id: in PSI_MI_TAG_INTERACTOR_ATTRIBUTE_ID 431 objPsi_MiNames: inside PSI_MI_TAG_NAMES 432 objPsi_MiXRef: inside PSI_MI_TAG_XREF 433 type: inside PSI_MI_TAG_TYPE 434 taxId: in PSI_MI_TAG_ORGANISM_ATTRIBUTE_TAX_ID 435 sequence: inside PSI_MI_TAG_SEQUENCE 436 """ 437 self.id = id # An integer represented as string 438 self.name = objPsi_MiNames 439 self.xRef = objPsi_MiXRef 440 self.type = objPsi_MiNamesType 441 self.taxId = taxId # An integer represented as string 442 self.sequence = sequence # A sequence of letters represented as string 443 return

444

445 - def __del__(self):

446 return

447

448 - def __str__(self):

449 return "{%s: %s, %s, %s, %s, %s}" % (self.id, self.name, self.xRef, self.type, self.taxId, self.sequence)

450 451 """ 452 ======================================================================================================= 453 Psi_MiInteraction OBJECT 454 """

455 -class Psi_MiInteraction:

456 """ 457 Class representing an interaction 458 """ 459 PSI_MI_TAG_INTERACTION = "interaction" 460 PSI_MI_TAG_INTERACTION_ATTRIBUTE_ID = "id" 461 PSI_MI_TAG_EXPERIMENT_LIST = "experimentList" 462 PSI_MI_TAG_EXPERIMENT_REFERENCE = "experimentRef" 463 PSI_MI_TAG_PARTICIPANT_LIST = "participantList" 464 PSI_MI_TAG_TYPE = "interactionType" 465 PSI_MI_TAG_NEGATIVE = "negative" 466

467 - def __init__(self, id=None, objPsi_MiNames=None, objPsi_MiXRef=None, listExperimentId=None, listObjPsi_MiParticipant=None, objPsi_MiXRefType=None, flagNegative=False):

468 """ 469 id: in PSI_MI_TAG_INTERACTION_ATTRIBUTE_ID 470 objPsi_MiNames: inside PSI_MI_TAG_NAMES 471 objPsi_MiXRef: inside PSI_MI_TAG_XREF 472 listExperimentId: inside PSI_MI_TAG_EXPERIMENT_LIST inside PSI_MI_TAG_EXPERIMENT_REFERENCE 473 listObjPsi_MiParticipant: inside PSI_MI_TAG_PARTICIPANT_LIST 474 type: inside PSI_MI_TAG_TYPE 475 """ 476 self.id = id # An integer represented as string 477 self.name = objPsi_MiNames 478 self.xRef = objPsi_MiXRef 479 if listExperimentId is None: # A list of integers (represented as string) corresponding to experiment ids 480 self.listExperimentId = [] 481 else: 482 self.listExperimentId = listExperimenId 483 if listObjPsi_MiParticipant is None: 484 self.listParticipant = [] 485 else: 486 self.listParticipant = listObjPsi_MiParticipant 487 self.type = objPsi_MiXRefType # Interaction type as xRef 488 self.negative = flagNegative 489 return

490

491 - def __del__(self):

492 return

493

494 - def __str__(self):

495 return "{%s: %s, %s, %s}" % (self.id, self.name, self.xRef, self.type, self.negative)

496

497 - def addParticipant(self, objPsi_MiParticipant):

498 self.listParticipant.append(objPsi_MiParticipant) 499 return

500 501 502 """ 503 ======================================================================================================= 504 Psi_MiParticipant OBJECT 505 """

506 -class Psi_MiParticipant:

507 """ 508 Class representing a participant 509 """ 510 PSI_MI_TAG_PARTICIPANT = "participant" 511 PSI_MI_TAG_PARTICIPANT_ATTRIBUTE_ID = "id" 512 PSI_MI_TAG_INTERACTOR_REFERENCE = "interactorRef" 513 PSI_MI_TAG_BIOLOGICAL_ROLE = "biologicalRole" 514 PSI_MI_TAG_EXPERIMENTAL_ROLE_LIST = "experimentalRoleList" 515 PSI_MI_TAG_EXPERIMENTAL_ROLE = "experimentalRole" 516

517 - def __init__(self, id=None, interactorReference=None, objPsi_MiNamesRoleBiological=None, listObjPsi_MiNamesRoleExperimental=None):

518 """ 519 id: in PSI_MI_TAG_INTERACTOR_ATTRIBUTE_ID 520 interactorId: inside PSI_MI_TAG_INTERACTOR_REFERENCE 521 objPsi_MiXRefRoleBiological: inside PSI_MI_TAG_BIOLOGICAL_ROLE inside PSI_MI_TAG_XREF 522 listObjPsi_MiXRefExperimentalRole: inside PSI_MI_TAG_EXPERIMENTAL_ROLE_LIST inside PSI_MI_TAG_EXPERIMENTAL_ROLE inside PSI_MI_TAG_XREF 523 """ 524 self.id = id # An integer represented as string 525 self.interactorId = interactorReference 526 self.nameRoleBiological = objPsi_MiNamesRoleBiological 527 if listObjPsi_MiNamesRoleExperimental is None: # A list of Psi_MiXRef objects corresponding to experiment roles 528 self.listNameRoleExperimental = [] 529 else: 530 self.listNameRoleExperimental = listObjPsi_MiNamesRoleExperimental 531 return

532

533 - def __del__(self):

534 return

535

536 - def __str__(self):

537 return "{%s: %s, %s}" % (self.id, self.interactorId, self.nameRoleBiological)

538 539 540 """ 541 ======================================================================================================= 542 Psi_MiNames OBJECT 543 """

544 -class Psi_MiNames:

545 """ 546 Class representing information encapsulated within names XML tags 547 """ 548 PSI_MI_TAG_NAMES = "names" 549 PSI_MI_TAG_LABEL = "shortLabel" 550 PSI_MI_TAG_NAME = "fullName" 551 PSI_MI_TAG_ALIAS = "alias" 552 PSI_MI_TAG_ALIAS_ATTRIBUTE_TYPE = "type" 553

554 - def __init__(self, label=None, name=None, listAlias=None):

555 """ 556 shortLabel: inside PSI_MI_TAG_LABEL 557 fullName: inside PSI_MI_TAG_NAME 558 listAlias: [(in PSI_MI_TAG_ALIAS_ATTRIBUTE_TYPE, inside PSI_MI_TAG_ALIAS), ] ---> i.e. [('gene name', 'Caf1'), ] 559 PSI_MI_TAG_ALIAS_ATTRIBUTE_TYPE can be: gene name | gene name snonym | orf name 560 561 """ 562 # self.dictName[self.PSI_MI_TAG_LABEL] = label 563 # self.dictName[self.PSI_MI_TAG_NAME] = name 564 # self.dictName[self.PSI_MI_TAG_ALIAS] = listAlias 565 self.label = label 566 self.name = name 567 if listAlias is None: 568 self.listAlias = [] 569 else: 570 self.listAlias = listAlias # A list of tuples in the format (type_string, id_string) 571 return

572

573 - def __del__(self):

574 return

575

576 - def __str__(self):

577 #return "%s" % self.dictName[PSI_MI_TAG_LABEL] 578 return "%s" % self.label

579 #return "%s %s %s" % (self.label, self.label, self.listAlias) 580 581 582 """ 583 ======================================================================================================= 584 Psi_MiXref OBJECT 585 """

586 -class Psi_MiXRef:

587 """ 588 Class representing information encapsulated within xref XML tags 589 """ 590 PSI_MI_TAG_XREF = "xref" 591 PSI_MI_TAG_REF_PRIMARY = "primaryRef" 592 PSI_MI_TAG_REF_SECONDARY = "secondaryRef" 593 PSI_MI_TAG_REF_ATTRIBUTE_DB = "db" 594 PSI_MI_TAG_REF_ATTRIBUTE_ID = "id" 595 PSI_MI_TAG_REF_ATTRIBUTE_TYPE = "refType" 596 PSI_MI_TAG_REF_ATTRIBUTE_SECONDARY = "secondary" 597

598 - def __init__(self, objDBReferenceRefPrimary=None, listObjDBReferenceRefSecondary=None):

599 """ 600 refPrimary: (in PSI_MI_TAG_REF_ATTRIBUTE_DB, in PSI_MI_TAG_REF_ATTRIBUTE_ID) 601 listRefSecondary: [(in PSI_MI_TAG_REF_ATTRIBUTE_DB, in PSI_MI_TAG_REF_ATTRIBUTE_ID), ] ---> i.e. [('go', 'GO:0035098')] 602 """ 603 self.refPrimary = objDBReferenceRefPrimary 604 if listObjDBReferenceRefSecondary is None: 605 self.listRefSecondary = [] 606 else: 607 self.listRefSecondary = listObjDBReferenceRefSecondary 608 return

609

610 - def __del__(self):

611 return

612

613 - def __str__(self):

614 return "%s" % (self.refPrimary)

615

616 -class DBReference:

617 """ 618 Class representing reference information to a database with db, id and type fields 619 """

620 - def __init__(self, db=None, id=None, type=None, secondary=None):

621 self.db = db 622 self.id = id 623 self.type = type 624 self.secondary = secondary 625 return

626

627 - def __del__(self):

628 return

629

630 - def __str__(self):

631 return "(%s, %s)" % (self.db, self.id)

632

Source Code for Module biana.BianaParser.psi_MiXMLParser