def createDefaults(self, file=None):
if file is None:
p = Parameters()
else:
p = Parameters(file)
self.gtfFileTextBox.setText(p.gtfFile)
self.refGenomeTextBox.setText(p.refGenome)
self.dbsnpTextBox.setText(p.dbsnp)
self.hapmapTextBox.setText(p.hapmap)
self.omniTextBox.setText(p.omni)
self.espTextBox.setText(p.esp)
self.aluRegionsTextBox.setText(p.aluRegions)
self.outputTextBox.setText(p.output)
self.sourceDirTextBox.setText(p.sourceDir)
self.threadsSpinBox.setValue(int(p.threads))
self.maxDiffSpinBox.setValue(float(p.maxDiff))
self.seedSpinBox.setValue(float(p.seedDiff))
self.standCallSpinBox.setValue(int(p.standCall))
self.standEmitSpinBox.setValue(int(p.standEmit))
self.intronDistanceSpinBox.setValue(int(p.intronDistance))
self.minPtsSpinBox.setValue(int(p.minPts))
self.epsSpinBox.setValue(int(p.eps))
self.pairedCheckBox.setChecked(p.paired)
self.keepTempCheckBox.setChecked(p.keepTemp)
self.overwriteCheckBox.setChecked(p.overwrite)
Helper.info("\t overwrite:" + str(self.params.overwrite), self.logFile)
Helper.info("", self.logFile)
if __name__ == '__main__':
if len(sys.argv) > 1:
parser = argparse.ArgumentParser(
prog = 'RnaEditor',
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''\
RnaEditor: easily detect editing sites from deep sequencing data'
----------------------------------------------------------------
run without arguments to start the user interface.
'''))
parser.add_argument('-i', '--input', metavar='Fastq-Files',nargs='+', type=str, help='Input fastq files (maximum two for paired-end sequencing)', required=True)
parser.add_argument('-c', '--conf', metavar='Configuration File', type=str, help='Configuration File used to read Parameters for RnaEditor', required=True, default='configuration.txt')
args = parser.parse_args()
parameters = Parameters(args.conf)
edit=RnaEdit(args.input,parameters,0)
edit.start()
edit.wait()
del edit
else:
pass
def newAssay(self):
"""
Function wich starts a new analysis
"""
global assay
inputTab = self.view.tabMainWindow.widget(0)
# get Parameters
parameters = Parameters(inputTab)
if parameters.paired:
# fastqs=inputTab.dropList.dropFirstTwoItems()
fastqs = inputTab.dropList.dropFirstItem()
if fastqs[0] is not None:
if not str(fastqs[0].text()).endswith(".bam"):
fastqs += inputTab.dropList.dropFirstItem()
else:
fastqs = inputTab.dropList.dropFirstItem()
"""
check if droplist returned a value
"""
if parameters.paired:
if fastqs[-1] is None:
QtGui.QMessageBox.information(
self.view, "Warning",
"Warning:\nNot enough Sequencing Files for paired-end sequencing!!!\n\nDrop FASTQ-Files to the drop area!"
)
return
if fastqs[0] is None:
QtGui.QMessageBox.information(
self.view, "Warning",
"Warning:\nNo Sequencing Files found!!!\n\nDrop FASTQ-Files to the drop area!"
)
return
sampleName = Helper.getSampleName(str(fastqs[0].text()))
if sampleName is None:
QtGui.QMessageBox.information(
self.view, "Warning",
"Warning:\nNo valid Sequencing File!!!\n\nDrop FASTQ-Files to the drop area!"
)
return
fastqFiles = []
for fastq in fastqs:
fastqFiles.append(str(fastq.text()))
runTab = RunTab(self)
# initialize new Thread with new assay
try:
assay = RnaEdit(fastqFiles, parameters, runTab.commandBox)
except Exception as err:
QtGui.QMessageBox.information(self.view, "Error",
str(err) + "Cannot start Analysis!")
Helper.error(str(err) + "\n creating rnaEditor Object Failed!",
textField=runTab.commandBox)
currentIndex = self.view.tabMainWindow.count()
# self.view.tabMainWindow.addTab(self.runTab, "Analysis"+ str(Helper.assayCount))
self.view.tabMainWindow.addTab(runTab,
sampleName + " " + str(currentIndex))
Helper.runningThreads.append(assay)
assay.start()
self.view.connect(assay, QtCore.SIGNAL("taskDone"), self.openAnalysis)