"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]
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())