Ejemplo n.º 1
0
                     "Otherwise, lines will be added for any individual mentioned in the file.")
 
 for k,d in Pedigree.REQUIRED_KEYS.iteritems():
     parser.add_argument('--%s'%k, type=str, dest=k, default=d, help='Override the column header for %s. Default is "%s".' % (k,d))
 for k,d in Pedigree.RESERVED_KEYS.iteritems():
     parser.add_argument('--%s'%k, type=str, dest=k, default=d, help='Override the column header for %s. Default is "%s".' % (k,d))
 
 args = parser.parse_args()
 
 for k in Pedigree.REQUIRED_KEYS.keys():
     Pedigree.REQUIRED_KEYS[k] = getattr(args,k)
 for k in Pedigree.RESERVED_KEYS.keys():
     Pedigree.RESERVED_KEYS[k] = getattr(args,k)
 
 print "Loading file..."
 ped = Pedigree(args.infile, countAndCalculate=True, zeroMissing=args.zeroMissing.strip().upper().startswith('T'), tickFunction=tick, numTicks = 100)
 print "Writing file..."
 lowPath = args.outfile.lower()
 if lowPath.endswith('.gexf'):
     edgeTypes = Pedigree.defaultEdgeTypes()
     nodeAttributeTypes = Pedigree.defaultNodeAttributeTypes()
     nodeAttributeTypes['is_root'] = gexf_node_attribute_mapper('is_root', attrType=gexf_node_attribute_mapper.BOOLEAN, defaultValue=False, validValues=[False,True])
     
     # Write the graph file
     ped.write_gexf(args.outfile, edgeTypes, nodeAttributeTypes)
 elif lowPath.endswith('.json'):
     ped.write_json(args.outfile)
 elif lowPath.endswith('.dot'):
     ped.write_dot(args.outfile)
 elif lowPath.endswith('.png'):
     program = lowPath[:-4].split('.')[-1]
Ejemplo n.º 2
0
 def go(self):
     global visWindow
     for k in Pedigree.REQUIRED_KEYS.keys():
         t = self.overrides[k].currentText()
         if t == '':
             self.displayError("%s header is required." % k)
             return
         elif not t in self.header:
             self.displayError("%s doesn't exist in the input file." % t)
             return
         Pedigree.REQUIRED_KEYS[k] = t
     for k in Pedigree.RESERVED_KEYS.keys():
         t = self.overrides[k].currentText()
         if self.window.programBox.currentText() == 'vis':
             if t == '':
                 self.displayError("%s header is required." % k)
                 return
             elif not t in self.header:
                 self.displayError("%s doesn't exist in the input file." % t)
                 return
         else:
             if t == '':
                 t = k
         Pedigree.RESERVED_KEYS[k] = t
     
     try:
         if self.window.programBox.currentText() == 'vis':
             fileName = self.window.inputField.text()
             if fileName.lower().endswith('.gexf') or fileName.lower().endswith('.json'):
                 raise Exception('.gexf and .json formats are not supported for the vis program. Use calculateD to create a .dat file.')
             ped = Pedigree(fileName, countAndCalculate=False, zeroMissing=self.window.zeroMissingBox.isChecked())
             from resources.main_app import App
             self.window.hide()
             visWindow = App(ped)
             self.window.close()
         else:
             progress = QProgressDialog(u"Running...", u"Cancel", 0, NUM_TICKS, parent=None)
             progress.setWindowModality(Qt.WindowModal)
             progress.show()
             
             def tick(newMessage=None, increment=1):
                 if progress.wasCanceled():
                     raise cancelException('Cancel clicked.')
                 newValue = min(progress.maximum(),progress.value()+increment)
                 progress.setValue(newValue)
                 if newMessage != None:
                     progress.setLabelText(newMessage)
                 return True
             
             ped = Pedigree(self.window.inputField.text(), countAndCalculate=True, zeroMissing=self.window.zeroMissingBox.isChecked(), tickFunction=tick, numTicks=NUM_TICKS)
             
             progress.setLabelText('Writing File...')
             extension = os.path.splitext(self.window.outputField.text())[1].lower()
             if extension == '.gexf':
                 edgeTypes = Pedigree.defaultEdgeTypes()
                 nodeAttributeTypes = Pedigree.defaultNodeAttributeTypes()
                 nodeAttributeTypes['is_root'] = gexf_node_attribute_mapper('is_root', attrType=gexf_node_attribute_mapper.BOOLEAN, defaultValue=False, validValues=[False,True])
                 ped.write_gexf(self.window.outputField.text(), edgeTypes, nodeAttributeTypes)
             elif extension == '.json':
                 ped.write_json(self.window.outputField.text())
             else:
                 ped.write_egopama(self.window.outputField.text())
             
             progress.close()
             
             self.window.inputField.setText(self.window.outputField.text())
             self.window.outputField.setText("")
             self.window.programBox.setCurrentIndex(1)
     except Exception, e:
         if not isinstance(e, cancelException):
             self.displayError("An unexpected error occurred.",traceback.format_exc())