def notifyRun(vcfPath, vcfAttributes, xAttribute, yAttribute, softFilters, forcedCategoricals, featurePaths):
global canceled, splash, window
splash = QProgressDialog("Loading %s" % os.path.split(vcfPath)[1], "Cancel", 0, 1000, parent=None)
splash.setWindowModality(Qt.WindowModal)
splash.setAutoReset(False)
splash.setAutoClose(False)
splash.show()
canceled = False
vData = variantData(vcfPath, vcfAttributes, forcedCategoricals)
vParams = variantLoadingParameters(passFunction=vData.addVariant,
rejectFunction=None,
callbackArgs={},
tickFunction=tick,
tickInterval=0.1,
individualsToInclude=[],
individualAppendString="",
lociToInclude=None,
mask=None,
invertMask=False,
attributesToInclude=None,
attributeAppendString="",
skipGenotypeAttributes=True,
returnFileObject=False,
alleleMatching=allele.STRICT,
attemptRepairsWhenComparing=True)
try:
variantFile.parseVcfFile(vcfPath, vParams)
except cancelButtonException:
splash.close()
window.window.show()
return
if softFilters == None:
softFilters = {}
for k in vData.axisLookups.iterkeys():
if k == xAttribute or k == yAttribute:
if vData.axisLookups[k].hasNumeric:
fivePercent = 0.05*(vData.axisLookups[k].maximum-vData.axisLookups[k].minimum)
ranges = [(vData.axisLookups[k].maximum-fivePercent,vData.axisLookups[k].maximum)]
else:
ranges = None
values = []
else:
ranges = None
values = None
softFilters[k] = valueFilter(values=values,
ranges=ranges,
includeNone=True,
includeBlank=True,
includeInf=True,
includeNaN=True,
includeMissing=True,
includeAlleleMasked=True,
listMode=valueFilter.LIST_INCLUSIVE)
intMan = interactionManager(vData,softFilters)
# TODO
fData = featureData(featurePaths)
if canceled:
splash.close()
window.window.show()
return
splash.close()
appWindow = appWidget(vData,fData,intMan,xAttribute,yAttribute)
intMan.setApp(appWindow)
class setupApp:
def __init__(self, params):
loader = QUiLoader()
infile = QFile("gui/ui/Setup.ui")
infile.open(QFile.ReadOnly)
self.window = loader.load(infile, None)
self.loadPrefs()
self.window.quitButton.clicked.connect(self.closeApp)
self.window.saveButton.clicked.connect(self.savePrefs)
self.window.runButton.clicked.connect(self.runSV)
self.splash = QProgressDialog("Loading", "Cancel", 0, 100, parent=None)
self.splash.setWindowModality(Qt.WindowModal)
self.splash.setAutoReset(False)
self.splash.setAutoClose(False)
self.splash.hide()
self.canceled = False
self.window.show()
self.runningApp = None
def loadPrefs(self):
infile = open(PREFS_FILE,'r')
self.window.textEdit.setPlainText(infile.read())
infile.close()
def savePrefs(self):
outfile=open(PREFS_FILE,'w')
outfile.write(self.window.textEdit.toPlainText())
outfile.close()
def showProgressWidget(self, estimate=100, message="Loading..."):
self.splash.setLabelText(message)
self.splash.setMaximum(estimate)
self.splash.setValue(0)
self.splash.show()
def tickProgressWidget(self, numTicks=1, message=None):
if self.canceled:
return
if message != None:
self.splash.setLabelText(message)
newValue = min(self.splash.maximum(),numTicks+self.splash.value())
self.splash.setValue(newValue)
self.canceled = self.splash.wasCanceled()
return self.canceled
def runSV(self, params=PREFS_FILE):
self.savePrefs()
self.window.hide()
appPrefs = prefs.generateFromText(self.window.textEdit.toPlainText())
self.showProgressWidget(appPrefs.maxTicks, "Loading files...")
self.canceled = False
vData = appPrefs.loadDataObjects(callback=self.tickProgressWidget)
if self.canceled:
self.splash.hide()
self.window.show()
return
self.showProgressWidget(vData.estimateTicks(), "Writing files...")
success = vData.dumpVcfFile(path='/Users/Home/Desktop/chr3-seq_parsed.vcf',callback=self.tickProgressWidget)
if not success:
self.splash.hide()
self.window.show()
return
sys.exit(0)
# TODO write to file
def closeApp(self):
self.window.reject()
