Description: Port to PyQt5
Bug-Debian: https://bugs.debian.org/935345
Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 06 Sep 2019 10:26:15 +0200

--- a/setup.py
+++ b/setup.py
@@ -1,9 +1,9 @@
 """ MicrobeGPS setup.py script. Allows direct installation of the tool or creating Python eggs. """
 
 try:
-	import PyQt4
+	import PyQt5
 except ImportError:
-	print('PyQt4 is not installed on your system! Please install PyQt4 first. You can download PyQt4 from http://www.riverbankcomputing.co.uk/software/pyqt/download or use your package manager to install the library.')
+	print('PyQt5 is not installed on your system!')
 	import sys
 	sys.exit()
 
--- a/microbegps/gui.py
+++ b/microbegps/gui.py
@@ -9,10 +9,10 @@ import pkg_resources
 import threading
 import pickle
 
-from PyQt4 import QtGui, QtCore
+from PyQt5 import QtGui, QtCore, QtWidgets
 
 import matplotlib.pyplot as plt
-from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas
 import matplotlib_venn as venn
 
 
@@ -79,7 +79,7 @@ First, a subset of reads is selected tha
 ]
 
 
-class Pipeline(QtGui.QWidget):
+class Pipeline(QtWidgets.QWidget):
 	def __init__(self,mainWindow):
 		super(Pipeline, self).__init__()
 		self.mainWindow = mainWindow
@@ -101,13 +101,13 @@ class Pipeline(QtGui.QWidget):
 						  self.step_visualize]
 		self.currentPipelineThread = None
 		
-		recipeLbl = QtGui.QLabel('Pipeline')
-		settingsLbl = QtGui.QLabel('Settings')
+		recipeLbl = QtWidgets.QLabel('Pipeline')
+		settingsLbl = QtWidgets.QLabel('Settings')
 
-		self.recipeList = QtGui.QListWidget()
+		self.recipeList = QtWidgets.QListWidget()
 		itemNames = ['Load Data', 'Raw Filter', 'Calculate Reference Table', 'Quality Filtering', 'Calculate Candidates', 'Visualize Results']	
 		for name in itemNames:
-			item = QtGui.QListWidgetItem(self.redIcon,name)
+			item = QtWidgets.QListWidgetItem(self.redIcon,name)
 			item.setFlags(QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable)
 			self.recipeList.addItem(item)
 		self.recipeList.setMinimumWidth(230)
@@ -116,119 +116,119 @@ class Pipeline(QtGui.QWidget):
 		
 
 		# create all settings pages
-		self.settingsBox = QtGui.QStackedWidget()
+		self.settingsBox = QtWidgets.QStackedWidget()
 
 		# page 0: load data
-		self.fileNameEdit = QtGui.QLineEdit()
-		selectButton = QtGui.QPushButton(self.openIcon,'')
+		self.fileNameEdit = QtWidgets.QLineEdit()
+		selectButton = QtWidgets.QPushButton(self.openIcon,'')
 		selectButton.clicked.connect(self.selectDirectory)
 		selectButton.setToolTip('Open directory containing SAM files')
-		sublayout = QtGui.QHBoxLayout()
+		sublayout = QtWidgets.QHBoxLayout()
 		sublayout.addWidget(self.fileNameEdit,stretch=4)
 		sublayout.addWidget(selectButton,stretch=1)
-		subwidget = QtGui.QWidget()
+		subwidget = QtWidgets.QWidget()
 		subwidget.setLayout(sublayout)
-		layout = QtGui.QGridLayout()
+		layout = QtWidgets.QGridLayout()
 		layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
-		layout.addWidget(QtGui.QLabel('Input Directory'),0,0)
+		layout.addWidget(QtWidgets.QLabel('Input Directory'),0,0)
 		layout.addWidget(subwidget,0,1)
-		loadDataWidget = QtGui.QWidget()
+		loadDataWidget = QtWidgets.QWidget()
 		loadDataWidget.setLayout(layout)
 		self.settingsBox.addWidget(loadDataWidget)
 
 		# page 1: Raw Filter
-		self.minSupportBox = QtGui.QSpinBox()
+		self.minSupportBox = QtWidgets.QSpinBox()
 		self.minSupportBox.setRange(1,1000000000)
 		self.minSupportBox.setValue(50)
 		self.minSupportBox.setMinimumWidth(100)
 		self.minSupportBox.valueChanged.connect(lambda: self.modifiedSettings(1))
-		self.maxMatchesBox = QtGui.QSpinBox()
+		self.maxMatchesBox = QtWidgets.QSpinBox()
 		self.maxMatchesBox.setRange(2,1000000000)
 		self.maxMatchesBox.setValue(80)
 		self.maxMatchesBox.setMinimumWidth(100)
 		self.maxMatchesBox.valueChanged.connect(lambda: self.modifiedSettings(1))
-		self.maxMappingError = QtGui.QDoubleSpinBox()
+		self.maxMappingError = QtWidgets.QDoubleSpinBox()
 		self.maxMappingError.setDecimals(2)
 		self.maxMappingError.setRange(0,1)
 		self.maxMappingError.setValue(1)
 		self.maxMappingError.setSingleStep(0.05)
 		self.maxMappingError.setMinimumWidth(100)
 		self.maxMappingError.valueChanged.connect(lambda: self.modifiedSettings(1))
-		self.mappingErrorQuantile = QtGui.QDoubleSpinBox()
+		self.mappingErrorQuantile = QtWidgets.QDoubleSpinBox()
 		self.mappingErrorQuantile.setDecimals(2)
 		self.mappingErrorQuantile.setRange(0,1)
 		self.mappingErrorQuantile.setValue(1)
 		self.mappingErrorQuantile.setSingleStep(0.05)
 		self.mappingErrorQuantile.setMinimumWidth(100)
 		self.mappingErrorQuantile.valueChanged.connect(lambda: self.modifiedSettings(1))
-		layout = QtGui.QFormLayout()
+		layout = QtWidgets.QFormLayout()
 		layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
-		layout.addRow(QtGui.QLabel('Minimum Genome Support'),self.minSupportBox)
-		layout.addRow(QtGui.QLabel('Max. Read Matches'),self.maxMatchesBox)
-		layout.addRow(QtGui.QLabel('Max. Read Mapping Error'),self.maxMappingError)
-		layout.addRow(QtGui.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)
-		rawFilterWidget = QtGui.QWidget()
+		layout.addRow(QtWidgets.QLabel('Minimum Genome Support'),self.minSupportBox)
+		layout.addRow(QtWidgets.QLabel('Max. Read Matches'),self.maxMatchesBox)
+		layout.addRow(QtWidgets.QLabel('Max. Read Mapping Error'),self.maxMappingError)
+		layout.addRow(QtWidgets.QLabel('Mapping Error Quantile'),self.mappingErrorQuantile)
+		rawFilterWidget = QtWidgets.QWidget()
 		rawFilterWidget.setLayout(layout)
 		self.settingsBox.addWidget(rawFilterWidget)
 		
 		# page 2: Calculate Reference Table
-		self.useIdMapping = QtGui.QRadioButton('No Mapping')
+		self.useIdMapping = QtWidgets.QRadioButton('No Mapping')
 		self.useIdMapping.toggled.connect(lambda: self.modifiedSettings(2))
-		self.useMappingFile = QtGui.QRadioButton('Mapping File')
+		self.useMappingFile = QtWidgets.QRadioButton('Mapping File')
 		self.useMappingFile.toggled.connect(lambda: self.modifiedSettings(2))
-		self.mappingFileEdit = QtGui.QLineEdit()
-		self.useNCBIFiles = QtGui.QRadioButton('NCBI catalog')
+		self.mappingFileEdit = QtWidgets.QLineEdit()
+		self.useNCBIFiles = QtWidgets.QRadioButton('NCBI catalog')
 		self.useNCBIFiles.setChecked(True)
 		self.useNCBIFiles.toggled.connect(lambda: self.modifiedSettings(2))
-		self.NCBICatalogPath = QtGui.QLineEdit('<default>')
+		self.NCBICatalogPath = QtWidgets.QLineEdit('<default>')
 		self.NCBICatalogPath.setToolTip('Clear this field to use the default catalog.')
-		selectButton1 = QtGui.QPushButton(self.openIcon,'')
+		selectButton1 = QtWidgets.QPushButton(self.openIcon,'')
 		selectButton1.clicked.connect(self.selectMappingFile)
 		selectButton1.setToolTip('Load Mapping File')
-		selectButton2 = QtGui.QPushButton(self.openIcon,'')
+		selectButton2 = QtWidgets.QPushButton(self.openIcon,'')
 		selectButton2.clicked.connect(self.selectNCBICatalog)
 		selectButton2.setToolTip('Load NCBI catalog file')
-		sublayout1 = QtGui.QHBoxLayout()
+		sublayout1 = QtWidgets.QHBoxLayout()
 		sublayout1.addWidget(self.mappingFileEdit,stretch=4)
 		sublayout1.addWidget(selectButton1,stretch=1)
-		subwidget1 = QtGui.QWidget()
+		subwidget1 = QtWidgets.QWidget()
 		subwidget1.setLayout(sublayout1)
-		sublayout2 = QtGui.QHBoxLayout()
+		sublayout2 = QtWidgets.QHBoxLayout()
 		sublayout2.addWidget(self.NCBICatalogPath,stretch=4)
 		sublayout2.addWidget(selectButton2,stretch=1)
-		subwidget2 = QtGui.QWidget()
+		subwidget2 = QtWidgets.QWidget()
 		subwidget2.setLayout(sublayout2)
-		layout = QtGui.QGridLayout()
+		layout = QtWidgets.QGridLayout()
 		layout.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
 		layout.addWidget(self.useIdMapping,0,0)
 		layout.addWidget(self.useMappingFile,1,0)
 		layout.addWidget(subwidget1,1,1)
 		layout.addWidget(self.useNCBIFiles,2,0)
 		layout.addWidget(subwidget2,2,1)
-		referenceTableWidget = QtGui.QWidget()
+		referenceTableWidget = QtWidgets.QWidget()
 		referenceTableWidget.setLayout(layout)
 		self.settingsBox.addWidget(referenceTableWidget)
 		
 		# page 3: Quality Filtering
-		self.minAbsoluteUnique = QtGui.QSpinBox()
+		self.minAbsoluteUnique = QtWidgets.QSpinBox()
 		self.minAbsoluteUnique.setRange(0,1000000000)
 		self.minAbsoluteUnique.setValue(20)
 		self.minAbsoluteUnique.setMinimumWidth(100)
 		self.minAbsoluteUnique.valueChanged.connect(lambda: self.modifiedSettings(3))
-		self.maxHomogeneity = QtGui.QDoubleSpinBox()
+		self.maxHomogeneity = QtWidgets.QDoubleSpinBox()
 		self.maxHomogeneity.setDecimals(3)
 		self.maxHomogeneity.setValue(0.6)
 		self.maxHomogeneity.setRange(0.,1.)
 		self.maxHomogeneity.setSingleStep(0.05)
 		self.maxHomogeneity.setMinimumWidth(100)
 		self.maxHomogeneity.valueChanged.connect(lambda: self.modifiedSettings(3))
-		self.minValidity = QtGui.QDoubleSpinBox()
-		layout = QtGui.QFormLayout()
+		self.minValidity = QtWidgets.QDoubleSpinBox()
+		layout = QtWidgets.QFormLayout()
 		layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
-		layout.addRow(QtGui.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)
-		layout.addRow(QtGui.QLabel('Max. Homogeneity'),self.maxHomogeneity)
+		layout.addRow(QtWidgets.QLabel('Min. Number Unique Reads'),self.minAbsoluteUnique)
+		layout.addRow(QtWidgets.QLabel('Max. Homogeneity'),self.maxHomogeneity)
 
-		qualFilterWidget = QtGui.QWidget()
+		qualFilterWidget = QtWidgets.QWidget()
 		qualFilterWidget.setLayout(layout)
 		self.settingsBox.addWidget(qualFilterWidget)
 		
@@ -239,75 +239,75 @@ class Pipeline(QtGui.QWidget):
 		self.minValidity.setSingleStep(0.05)
 		self.minValidity.setMinimumWidth(100)
 		self.minValidity.valueChanged.connect(lambda: self.modifiedSettings(4))
-		self.coverageSimilarity = QtGui.QDoubleSpinBox()
+		self.coverageSimilarity = QtWidgets.QDoubleSpinBox()
 		self.coverageSimilarity.setDecimals(2)
 		self.coverageSimilarity.setValue(0.2)
 		self.coverageSimilarity.setMinimum(0)
 		self.coverageSimilarity.setSingleStep(0.05)
 		self.coverageSimilarity.setMinimumWidth(100)
 		self.coverageSimilarity.valueChanged.connect(lambda: self.modifiedSettings(4))
-		self.sharedFractionUSR = QtGui.QDoubleSpinBox()
+		self.sharedFractionUSR = QtWidgets.QDoubleSpinBox()
 		self.sharedFractionUSR.setDecimals(2)
 		self.sharedFractionUSR.setValue(0.2)	
 		self.sharedFractionUSR.setRange(0.,1.)
 		self.sharedFractionUSR.setSingleStep(0.05)
 		self.sharedFractionUSR.setMinimumWidth(100)
 		self.sharedFractionUSR.valueChanged.connect(lambda: self.modifiedSettings(4))
-		self.sharedFractionAll = QtGui.QDoubleSpinBox()
+		self.sharedFractionAll = QtWidgets.QDoubleSpinBox()
 		self.sharedFractionAll.setDecimals(2)
 		self.sharedFractionAll.setValue(0.6)	
 		self.sharedFractionAll.setRange(0.,1.)
 		self.sharedFractionAll.setSingleStep(0.05)
 		self.sharedFractionAll.setMinimumWidth(100)
 		self.sharedFractionAll.valueChanged.connect(lambda: self.modifiedSettings(4))
-		layout = QtGui.QFormLayout()
+		layout = QtWidgets.QFormLayout()
 		layout.setFormAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
-		layout.addRow(QtGui.QLabel('Min. Genome Validity'),self.minValidity)
-		layout.addRow(QtGui.QLabel('Coverage Similarity'),self.coverageSimilarity)
-		layout.addRow(QtGui.QLabel('Fraction Shared USR'),self.sharedFractionUSR)
-		layout.addRow(QtGui.QLabel('Fraction Shared Reads'),self.sharedFractionAll)
-		extractUSRWidget = QtGui.QWidget()
+		layout.addRow(QtWidgets.QLabel('Min. Genome Validity'),self.minValidity)
+		layout.addRow(QtWidgets.QLabel('Coverage Similarity'),self.coverageSimilarity)
+		layout.addRow(QtWidgets.QLabel('Fraction Shared USR'),self.sharedFractionUSR)
+		layout.addRow(QtWidgets.QLabel('Fraction Shared Reads'),self.sharedFractionAll)
+		extractUSRWidget = QtWidgets.QWidget()
 		extractUSRWidget.setLayout(layout)
 		self.settingsBox.addWidget(extractUSRWidget)
 		
 		# page 5: Visualize
-		self.closeOnFinish = QtGui.QCheckBox('Close this window after visualizing results')
-		layout = QtGui.QVBoxLayout()
+		self.closeOnFinish = QtWidgets.QCheckBox('Close this window after visualizing results')
+		layout = QtWidgets.QVBoxLayout()
 		layout.addWidget(self.closeOnFinish)
-		visualizeWidget = QtGui.QWidget()
+		visualizeWidget = QtWidgets.QWidget()
 		visualizeWidget.setLayout(layout)
 		self.settingsBox.addWidget(visualizeWidget)		
 		
 		# Text boxes
-		self.descriptionText = QtGui.QTextEdit()
+		self.descriptionText = QtWidgets.QTextEdit()
 		self.descriptionText.setReadOnly(True)
 		
-		self.consoleText = QtGui.QTextEdit()
+		self.consoleText = QtWidgets.QTextEdit()
 		self.consoleText.setReadOnly(True)
 		consoleFont = self.consoleText.font()
 		consoleFont.setPointSize(self.font().pointSize()-1)
 		self.consoleText.setFont(consoleFont)
 		
 		# Progress bar
-		self.progress = QtGui.QProgressBar()
+		self.progress = QtWidgets.QProgressBar()
 		
-		consoleLayout = QtGui.QVBoxLayout()
+		consoleLayout = QtWidgets.QVBoxLayout()
 		consoleLayout.addWidget(self.progress)
 		consoleLayout.addWidget(self.consoleText)
-		consoleWidget = QtGui.QWidget()
+		consoleWidget = QtWidgets.QWidget()
 		consoleWidget.setLayout(consoleLayout)
 
-		self.runStepBtn = QtGui.QPushButton("Run Step")
+		self.runStepBtn = QtWidgets.QPushButton("Run Step")
 		self.runStepBtn.clicked.connect(self.runOneStep)
-		self.runPipelineBtn = QtGui.QPushButton("Run Pipeline")
+		self.runPipelineBtn = QtWidgets.QPushButton("Run Pipeline")
 		self.runPipelineBtn.clicked.connect(self.runPipeline)
-		buttonLayout = QtGui.QHBoxLayout()
+		buttonLayout = QtWidgets.QHBoxLayout()
 		buttonLayout.addWidget(self.runStepBtn)
 		buttonLayout.addWidget(self.runPipelineBtn)
-		buttonBar = QtGui.QWidget()
+		buttonBar = QtWidgets.QWidget()
 		buttonBar.setLayout(buttonLayout)
 		
-		gridLayout = QtGui.QGridLayout()
+		gridLayout = QtWidgets.QGridLayout()
 		gridLayout.setColumnStretch(0,2)
 		gridLayout.setColumnStretch(1,2)
 		gridLayout.addWidget(recipeLbl,0,0)
@@ -343,7 +343,7 @@ class Pipeline(QtGui.QWidget):
 			try:
 				target_table,read_table = gps.read_sam_files_no_pysam(directory,status_reporter)
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit(target_table,read_table)
@@ -389,7 +389,7 @@ class Pipeline(QtGui.QWidget):
 						pr=printer)
 				gps.calculate_mapping_statistics(p.target_table)
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit()
@@ -441,7 +441,7 @@ class Pipeline(QtGui.QWidget):
 				else:
 					ref_table = gps.get_reference_table(p.target_table,p.read_table)	
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit(ref_table)
@@ -488,7 +488,7 @@ class Pipeline(QtGui.QWidget):
 				gps.filter_ref_table(p.ref_table,p.read_table,custom_filt1,printer)
 				#GpsTools.calculate_valcov(p.ref_table,printer)
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit()
@@ -549,7 +549,7 @@ class Pipeline(QtGui.QWidget):
 				group_dict = gps.create_groups_dc(usr_mat,all_mat,n2i,p.sharedFractionUSR.value(),status=printer)
 				candidates = gps.enrich_groups(group_dict,p.ref_table,p.read_table,i2n)
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit(candidates)
@@ -591,7 +591,7 @@ class Pipeline(QtGui.QWidget):
 				p.mainWindow.visualize(p.candidates,p.ref_table,p.read_table)
 				p.mainWindow.settings_pipeline = p.get_settings()
 			except Exception as e:
-				self.failed.emit(e.message)
+				self.failed.emit(str(e))
 				raise
 			else:
 				self.done.emit()
@@ -646,7 +646,7 @@ class Pipeline(QtGui.QWidget):
 			try:
 				target_table,read_table = gps.read_sam_files_no_pysam(directory,self.status.emit)
 			except Exception as e:
-				self.failed.emit(0,e.message)
+				self.failed.emit(0,str(e))
 				raise
 			else:
 				self.done.emit(0)
@@ -664,7 +664,7 @@ class Pipeline(QtGui.QWidget):
 						pr=p.pr)
 				gps.calculate_mapping_statistics(target_table)
 			except Exception as e:
-				self.failed.emit(1,e.message)
+				self.failed.emit(1,str(e))
 				raise
 			else:
 				self.done.emit(1)
@@ -686,7 +686,7 @@ class Pipeline(QtGui.QWidget):
 				else:
 					ref_table = gps.get_reference_table(target_table,read_table)	
 			except Exception as e:
-				self.failed.emit(2,e.message)
+				self.failed.emit(2,str(e))
 				raise
 			else:
 				self.done.emit(2)
@@ -703,7 +703,7 @@ class Pipeline(QtGui.QWidget):
 					return True
 				gps.filter_ref_table(ref_table,read_table,custom_filt1,p.pr)
 			except Exception as e:
-				self.failed.emit(3,e.message)
+				self.failed.emit(3,str(e))
 				raise
 			else:
 				self.done.emit(3)
@@ -730,7 +730,7 @@ class Pipeline(QtGui.QWidget):
 				group_dict = gps.create_groups_dc(usr_mat,all_mat,n2i,p.sharedFractionUSR.value(),status=p.pr)
 				candidates = gps.enrich_groups(group_dict,ref_table,read_table,i2n)
 			except Exception as e:
-				self.failed.emit(4,e.message)
+				self.failed.emit(4,str(e))
 				raise
 			else:
 				self.done.emit(4)
@@ -742,7 +742,7 @@ class Pipeline(QtGui.QWidget):
 				p.mainWindow.visualize(candidates,ref_table,read_table)
 				p.mainWindow.settings_pipeline = p.get_settings()
 			except Exception as e:
-				self.failed.emit(5,e.message)
+				self.failed.emit(5,str(e))
 				raise
 			else:
 				self.done.emit(5)
@@ -805,14 +805,14 @@ class Pipeline(QtGui.QWidget):
 		self.stepsDone = min(step-1,self.stepsDone)
 
 	def selectDirectory(self):
-		fname = str(QtGui.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))
+		fname = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select input directory',parent=self))
 		if len(fname):
 			self.pr("Input directory for SAM files: "+fname)
 			self.fileNameEdit.setText(fname)
 			self.modifiedSettings(0)
 
 	def selectMappingFile(self):
-		fname = str(QtGui.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))
+		fname = str(QtWidgets.QFileDialog().getOpenFileName(caption='Load ID Mapping File',filter='Tab separated text files (*)',parent=self))
 		if len(fname):
 			self.pr("Using ID Mapping File "+fname)
 			self.mappingFileEdit.setText(fname)
@@ -820,7 +820,7 @@ class Pipeline(QtGui.QWidget):
 			self.useMappingFile.setChecked(True)
 
 	def selectNCBICatalog(self):
-		fname = str(QtGui.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))
+		fname = str(QtWidgets.QFileDialog().getOpenFileName(directory='data/taxonomy/',caption='Select NCBI catalog file',parent=self))
 		if len(fname):
 			self.pr("Using NCBI catalog "+fname)
 			self.NCBICatalogPath.setText(fname)
@@ -871,7 +871,7 @@ class Pipeline(QtGui.QWidget):
 		self.sharedFractionAll.setValue(settings.get('fraction_shared_all',0.8))
 
 
-class GPSAnalyzer(QtGui.QMainWindow):
+class GPSAnalyzer(QtWidgets.QMainWindow):
 	def __init__(self):
 		super(GPSAnalyzer, self).__init__()
 		self.initUI()
@@ -889,7 +889,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 				mod = importer.find_module(mod_name).load_module(mod_name)
 				modules_d[mod_name] = mod.GPSModule(self)
 			except Exception as e:
-				self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,e.message))			
+				self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,str(e)))			
 		self.modules = modules_d
 		if len(self.modules) > 0:
 			self.pr('Loaded modules: <i>%s</i>'%(', '.join(iter(self.modules.keys()))))
@@ -898,22 +898,22 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		self.pipelineGui = Pipeline(self)
 		
 		# Prepare the Docks on the right hand side
-		self.graphicDock = QtGui.QDockWidget('Graphic',self)
-		self.graphicDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+		self.graphicDock = QtWidgets.QDockWidget('Graphic',self)
+		self.graphicDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
 		self.graphicDock.setMinimumSize(450,300)
-		self.graphicDock.setTitleBarWidget(QtGui.QWidget())
+		self.graphicDock.setTitleBarWidget(QtWidgets.QWidget())
 		
-		self.toolsDock = QtGui.QDockWidget('Tools',self)
-		self.toolsDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+		self.toolsDock = QtWidgets.QDockWidget('Tools',self)
+		self.toolsDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
 		self.toolsDock.setMinimumHeight(150)
 		self.toolsDock.setMaximumHeight(250)
-		self.toolsDock.setTitleBarWidget(QtGui.QWidget())
+		self.toolsDock.setTitleBarWidget(QtWidgets.QWidget())
 
-		self.consoleDock = QtGui.QDockWidget('Console',self)
-		self.consoleDock.setFeatures(QtGui.QDockWidget.NoDockWidgetFeatures)
+		self.consoleDock = QtWidgets.QDockWidget('Console',self)
+		self.consoleDock.setFeatures(QtWidgets.QDockWidget.NoDockWidgetFeatures)
 		self.consoleDock.setMinimumHeight(150)
 		self.consoleDock.setMaximumHeight(450)
-		self.consoleDock.setTitleBarWidget(QtGui.QWidget())
+		self.consoleDock.setTitleBarWidget(QtWidgets.QWidget())
 		
 		self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.graphicDock)
 		self.addDockWidget(QtCore.Qt.RightDockWidgetArea,self.toolsDock)
@@ -924,72 +924,72 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		self.figure = plt.figure()
 		self.canvas = FigureCanvas(self.figure)
 		
-		self.phyloTreeWidget = QtGui.QTreeWidget()
+		self.phyloTreeWidget = QtWidgets.QTreeWidget()
 		self.phyloTreeWidget.setHeaderHidden(True)
 		self.phyloTreeWidget.setUniformRowHeights(False)
 		self.phyloTreeWidget.setAutoScrollMargin(50)
-		self.phyloTreeWidget.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
-		self.phyloTreeWidget.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
+		self.phyloTreeWidget.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
+		self.phyloTreeWidget.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
 		self.phyloTreeWidget.setMouseTracking(True)
 		self.phyloTreeWidget.itemClicked.connect(self.view_tree_selection)
 		self.phyloTreeWidget.setColumnCount(2)
 		self.phyloTreeWidget.itemCollapsed.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))
 		self.phyloTreeWidget.itemExpanded.connect(lambda x: self.phyloTreeWidget.resizeColumnToContents(0))
 
-		self.graphicsTab = QtGui.QTabWidget()
-		self.graphicsTab.setTabPosition(QtGui.QTabWidget.South)
+		self.graphicsTab = QtWidgets.QTabWidget()
+		self.graphicsTab.setTabPosition(QtWidgets.QTabWidget.South)
 		self.graphicsTab.addTab(self.canvas,"Figure")
 		self.graphicsTab.addTab(self.phyloTreeWidget,"Tree")
 		
 		self.graphicDock.setWidget(self.graphicsTab)	
 		
 		# Fill the Tools Dock
-		self.enablePlottingBox = QtGui.QCheckBox('Draw Graphics')
+		self.enablePlottingBox = QtWidgets.QCheckBox('Draw Graphics')
 		self.enablePlottingBox.setChecked(True)
-		self.enableTaxonomyTree = QtGui.QCheckBox('Interactive Tree')
+		self.enableTaxonomyTree = QtWidgets.QCheckBox('Interactive Tree')
 		self.enableTaxonomyTree.setChecked(True)
 		
-		exportFigureQualityLabel = QtGui.QLabel('Image export quality (DPI)')
-		self.exportFigureQuality = QtGui.QSpinBox()
+		exportFigureQualityLabel = QtWidgets.QLabel('Image export quality (DPI)')
+		self.exportFigureQuality = QtWidgets.QSpinBox()
 		self.exportFigureQuality.setMinimum(10)
 		self.exportFigureQuality.setMaximum(1200)
 		self.exportFigureQuality.setValue(150)
 		self.exportFigureQuality.setSingleStep(10)
 		
-		showPipelineBtn = QtGui.QPushButton('Show GPS Pipeline')
+		showPipelineBtn = QtWidgets.QPushButton('Show GPS Pipeline')
 		showPipelineBtn.clicked.connect(self.pipelineGui.show)
 
-		toolsGrid = QtGui.QGridLayout()
+		toolsGrid = QtWidgets.QGridLayout()
 		toolsGrid.addWidget(self.enablePlottingBox,0,0)
 		toolsGrid.addWidget(self.enableTaxonomyTree,0,1)
 		toolsGrid.addWidget(exportFigureQualityLabel,1,0)
 		toolsGrid.addWidget(self.exportFigureQuality,1,1)
 		toolsGrid.addWidget(showPipelineBtn,2,0)
 
-		toolsWidget = QtGui.QWidget()
+		toolsWidget = QtWidgets.QWidget()
 		toolsWidget.setLayout(toolsGrid)
 		
-		self.toolsTab = QtGui.QTabWidget()
+		self.toolsTab = QtWidgets.QTabWidget()
 		self.toolsTab.currentChanged.connect(self.show_module_help)
-		self.toolsTab.setTabPosition(QtGui.QTabWidget.South)
+		self.toolsTab.setTabPosition(QtWidgets.QTabWidget.South)
 		self.toolsTab.addTab(toolsWidget,"Settings")
 
 		self.toolsDock.setWidget(self.toolsTab)
 		
 		# Fill the Console Dock
-		self.helpText = QtGui.QTextEdit()
+		self.helpText = QtWidgets.QTextEdit()
 		self.helpText.setReadOnly(True)
-		self.consoleText = QtGui.QTextBrowser()
+		self.consoleText = QtWidgets.QTextBrowser()
 		self.consoleText.setReadOnly(True)
 		
-		self.textTabs = QtGui.QTabWidget()
-		self.textTabs.setTabPosition(QtGui.QTabWidget.South)
+		self.textTabs = QtWidgets.QTabWidget()
+		self.textTabs.setTabPosition(QtWidgets.QTabWidget.South)
 		self.textTabs.addTab(self.helpText,"Help")
 		self.textTabs.addTab(self.consoleText,"Console")
 		self.consoleDock.setWidget(self.textTabs)
 		
 		# Insert the main Tree Widget
-		self.treeView = QtGui.QTreeWidget()
+		self.treeView = QtWidgets.QTreeWidget()
 		self.treeView.setColumnCount(7)
 		self.treeView.setColumnWidth(0,300)
 		self.treeView.setHeaderLabels(['Name','Reads','Unique','Coverage','Validity','Homogeneity','Mapping Error'])
@@ -998,52 +998,52 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		self.treeView.itemSelectionChanged.connect(self.selection_changed_handler)
 		self.treeView.setUniformRowHeights(False)
 		self.treeView.setAutoScrollMargin(50)
-		self.treeView.setSelectionMode(QtGui.QAbstractItemView.ExtendedSelection)
-		self.treeView.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
+		self.treeView.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
+		self.treeView.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
 		self.treeView.setMinimumWidth(400)
 		self.treeView.setMouseTracking(True)
-		self.treeView.header().setClickable(True)
+		self.treeView.header().setSectionsClickable(True)
 		self.treeView.header().sectionClicked.connect(self.show_header_help)
 		self.setCentralWidget(self.treeView)
 
 		# New Analysis action
-		new_analysis = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)
+		new_analysis = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/run.png')), 'New Analysis', self)
 		new_analysis.triggered.connect(self.new_analysis)
 		
 		# Load Data action
-		load_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)
+		load_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/open.png')), 'Load Data', self)
 		load_data.triggered.connect(self.load_data)
 		
 		# Save Data action
-		save_data = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)
+		save_data = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/save.png')), 'Save Data', self)
 		save_data.triggered.connect(self.save_data)
 		
 		# Exit Program action
-		exit_program = QtGui.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)
+		exit_program = QtWidgets.QAction(QtGui.QIcon(pkg_resources.resource_filename('microbegps','data/gui/exit.png')), 'Exit', self)
 		exit_program.triggered.connect(self.close)
 		
 		# Export iTOL tree
-		export_iTOL_tree = QtGui.QAction('Export Tree to iTOL', self)
+		export_iTOL_tree = QtWidgets.QAction('Export Tree to iTOL', self)
 		export_iTOL_tree.setToolTip('Export a set of files that can be loaded with the online tree visualizer iTOL.')
 		export_iTOL_tree.triggered.connect(self.export_iTOL)
 
 		# Export current graphic
-		export_graphic = QtGui.QAction('Export Figure', self)
+		export_graphic = QtWidgets.QAction('Export Figure', self)
 		export_graphic.setToolTip('Export the figure currently shown in the graphics panel to file.')
 		export_graphic.triggered.connect(self.export_graphic)
 
 		# Show the program information on the console
-		show_program_info = QtGui.QAction('About MicrobeGPS', self)
+		show_program_info = QtWidgets.QAction('About MicrobeGPS', self)
 		show_program_info.setToolTip('Show the program information on the console.')
 		show_program_info.triggered.connect(self.show_program_info)
 
 		# Load online help
-		show_online_help = QtGui.QAction('Online help', self)
+		show_online_help = QtWidgets.QAction('Online help', self)
 		show_online_help.setToolTip('Redirect to the online help of MicrobeGPS.')
 		show_online_help.triggered.connect(self.show_online_help)
 		
 		# Show the license on the console
-		show_license = QtGui.QAction('Show License', self)
+		show_license = QtWidgets.QAction('Show License', self)
 		show_license.setToolTip('Show the licensing information on the console.')
 		show_license.triggered.connect(self.show_license)
 		
@@ -1079,18 +1079,18 @@ class GPSAnalyzer(QtGui.QMainWindow):
 	def closeEvent(self, event):
 		if self.saving:
 			quit_msg = "Data saving in progress. Are you sure you want to exit the program? Unsaved data will be lost!"
-			reply = QtGui.QMessageBox.question(self, 'Message', 
-	                  quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
-			if reply == QtGui.QMessageBox.Yes:
+			reply = QtWidgets.QMessageBox.question(self, 'Message', 
+	                  quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
+			if reply == QtWidgets.QMessageBox.Yes:
 				event.accept()
 				self.pipelineGui.close()
 			else:
 				event.ignore()			
 		else:
 			quit_msg = "Are you sure you want to exit the program?"
-			reply = QtGui.QMessageBox.question(self, 'Message', 
-	                  quit_msg, QtGui.QMessageBox.Yes, QtGui.QMessageBox.No)
-			if reply == QtGui.QMessageBox.Yes:
+			reply = QtWidgets.QMessageBox.question(self, 'Message', 
+	                  quit_msg, QtWidgets.QMessageBox.Yes, QtWidgets.QMessageBox.No)
+			if reply == QtWidgets.QMessageBox.Yes:
 				event.accept()
 				self.pipelineGui.close()
 			else:
@@ -1129,7 +1129,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 				#  find member with most unique reads -> use as representative
 				most_unique = max([(m,grp.members[m].unique) for m in grp.members],key=lambda x:x[1])
 				cand_name = most_unique[0]
-			gr_item = QtGui.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),
+			gr_item = QtWidgets.QTreeWidgetItem(self.treeView,['Cand. %i: %s (%i)'%(g+1,cand_name,n_mem),
 					'%i'%grp.reads,'%i'%grp.unique, '%f'%grp.cov, '%f'%grp.max_val,
 					'%f'%grp.cov_homog, '%f'%grp.map_qual],QtCore.Qt.AlignHCenter)
 			gr_item.setIcon(0,candidateIcon)
@@ -1153,7 +1153,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 			for m in sorted_members:
 				mbr = grp.members[m]
 				self.mapq = [min(self.mapq[0],mbr.map_qual),max(self.mapq[1],mbr.map_qual)]
-				m_item = QtGui.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,
+				m_item = QtWidgets.QTreeWidgetItem(gr_item,[m,'%i'%mbr.reads,
 					'%i'%mbr.unique, '%f'%mbr.coverage, '%f'%mbr.validity,
 					'%f'%mbr.cov_homog, '%f'%mbr.map_qual])
 				m_item.setIcon(0,sequenceIcon)
@@ -1168,13 +1168,13 @@ class GPSAnalyzer(QtGui.QMainWindow):
 				for i in range(1,m_item.columnCount()):
 					m_item.setTextColor(i,QtCore.Qt.black)
 				# Sub-Item: all reads
-				ar_item = QtGui.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])
+				ar_item = QtWidgets.QTreeWidgetItem(m_item,['All reads (%i)'%mbr.reads])
 				ar_item.i_type = "all reads"
 				# Sub-Item: unique reads
-				ur_item = QtGui.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])
+				ur_item = QtWidgets.QTreeWidgetItem(m_item,['Unique reads (%i)'%mbr.unique])
 				ur_item.i_type = "unique reads"
 				# Sub-Item: Top Shared Genomes
-				rg_item = QtGui.QTreeWidgetItem(m_item,['Related genomes'])
+				rg_item = QtWidgets.QTreeWidgetItem(m_item,['Related genomes'])
 				rg_item.i_type = "related"
 
 		# Iterate over all items and colorize the fields
@@ -1182,19 +1182,19 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		for g in range(root.childCount()):
 			group = root.child(g)
 			frac = int(255*(1.-group.unique/float(group.reads)))
-			group.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
+			group.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
 			for m in range(group.childCount()):
 				m_item = group.child(m)
 				frac = 255-int(m_item.unique/float(m_item.reads)*255)
-				m_item.setBackground(2,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
+				m_item.setBackground(2,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
 				frac = int(255*(1-m_item.validity))
-				m_item.setBackground(4,QtGui.QBrush(QtGui.QColor(frac,255,frac)))
+				m_item.setBackground(4,QtWidgets.QBrush(QtWidgets.QColor(frac,255,frac)))
 				frac = int(128.*(m_item.map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
-				m_item.setBackground(6,QtGui.QBrush(QtGui.QColor(127+frac,255-frac,0)))
+				m_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(127+frac,255-frac,0)))
 
 				d_max = math.sqrt(math.log(2/0.05))/math.sqrt(2*m_item.reads)
 				if m_item.cov_homog < d_max:
-					m_item.setBackground(5,QtGui.QBrush(QtGui.QColor(0,0,255)))
+					m_item.setBackground(5,QtWidgets.QBrush(QtWidgets.QColor(0,0,255)))
 					m_item.setTextColor(5,QtCore.Qt.white)
 					
 		# Build the taxonomy tree for all observed genomes
@@ -1216,7 +1216,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 					continue
 				if not tid in self.taxid_to_item:
 					# add item to tree if not already found
-					self.taxid_to_item[tid] = QtGui.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])
+					self.taxid_to_item[tid] = QtWidgets.QTreeWidgetItem(par,[self.taxonomy_names.get(tid,'[Not found]')])
 				par = self.taxid_to_item[tid]
 
 				
@@ -1235,10 +1235,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
 				for rd in reads:
 					map_qual = reads[rd]
 					num_matches = len(self.reads[rd].matches)
-					rd_item = QtGui.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])
+					rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'%i'%num_matches,'','','','','%f'%map_qual])
 					rd_item.i_type = "read"
 					frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
-					rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+					rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
 			if item.i_type == "unique reads":
 				ref_name = str(item.parent().text(0))
 				self.pr("Collecting all unique reads for "+ref_name,False)
@@ -1250,10 +1250,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
 							reads[rd] = trg.reads[rd][2]
 				for rd in reads:
 					map_qual = reads[rd]
-					rd_item = QtGui.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])
+					rd_item = QtWidgets.QTreeWidgetItem(item,[rd,'','','','','','%f'%map_qual])
 					rd_item.i_type = "unique read"
 					frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
-					rd_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+					rd_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
 			if item.i_type == "read":
 				rd_name = str(item.text(0))
 				self.pr("Collecting all matches of read "+rd_name,False)
@@ -1263,10 +1263,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
 						if rd_name in trg.reads:
 							map_qual = trg.reads[rd_name][2]
 							break
-					mt_item = QtGui.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])
+					mt_item = QtWidgets.QTreeWidgetItem(item,[mtc,'','','','','','%f'%map_qual])
 					mt_item.i_type = "match"
 					frac = int(128.*(map_qual-self.mapq[0])/(self.mapq[1]-self.mapq[0]))
-					mt_item.setBackground(6,QtGui.QBrush(QtGui.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
+					mt_item.setBackground(6,QtWidgets.QBrush(QtWidgets.QColor(max(0,min(127+frac,255)),min(max(255-frac,0),255),0)))
 			if item.i_type == "match":
 				match_name = str(item.text(0))
 				group_id = self.ref2group[match_name]
@@ -1292,10 +1292,10 @@ class GPSAnalyzer(QtGui.QMainWindow):
 				# Sort by size, descending
 				sorted_names = sorted([(d,related[d]) for d in related],key=lambda x:-x[1])
 				for name,shared in sorted_names:
-					mt_item = QtGui.QTreeWidgetItem(item,[name,'%i'%shared])
+					mt_item = QtWidgets.QTreeWidgetItem(item,[name,'%i'%shared])
 					mt_item.i_type = "match"
 					frac = int(255*(1-shared/float(self.references[ref_name].reads)))
-					mt_item.setBackground(1,QtGui.QBrush(QtGui.QColor(255,frac,frac)))
+					mt_item.setBackground(1,QtWidgets.QBrush(QtWidgets.QColor(255,frac,frac)))
 					
 	
 	def tree_item_clicked_handler(self,item,column):
@@ -1492,7 +1492,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 			# now color the tree
 			for taxid,item in self.taxid_to_item.items():
 				if not taxid == 1:
-					item.setBackground(0,QtGui.QBrush(QtGui.QColor(255,255,255)))
+					item.setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(255,255,255)))
 					item.setText(1,'')
 			if 1 in reads:
 				total_reads = float(len(reads[1]))
@@ -1501,7 +1501,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 						N_reads = len(reads.get(taxid,set()))
 						frac =100+ int((1.-N_reads/total_reads)*155)
 						if taxid in self.taxid_to_item:
-							self.taxid_to_item[taxid].setBackground(0,QtGui.QBrush(QtGui.QColor(frac,frac,255)))
+							self.taxid_to_item[taxid].setBackground(0,QtWidgets.QBrush(QtWidgets.QColor(frac,frac,255)))
 							self.phyloTreeWidget.expandItem(self.taxid_to_item[taxid])
 							self.taxid_to_item[taxid].setText(1,'%i'%N_reads)
 			self.phyloTreeWidget.resizeColumnToContents(0)
@@ -1570,7 +1570,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 					#nodes,ranks = taxonomy.parse_nodes_dmp(gzip.open('data/taxonomy/nodes.dmp.gz','r'))
 					nodes,ranks = taxonomy.parse_nodes_dmp(pkg_resources.resource_stream('microbegps','data/taxonomy/nodes.dmp'))
 				except Exception as e:
-					self.failed.emit('<b><font color="DarkRed">Error loading NCBI taxonomy!</font></b><br>Message: <i>'+e.message+'</i>')
+					self.failed.emit('<b><font color="DarkRed">Error loading NCBI taxonomy!</font></b><br>Message: <i>'+str(e)+'</i>')
 					raise
 				else:
 					self.done.emit(nodes,ranks)
@@ -1584,7 +1584,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 					#target = taxonomy.parse_names_dmp(gzip.open('data/taxonomy/names.dmp.gz','r'))
 					target = taxonomy.parse_names_dmp(pkg_resources.resource_stream('microbegps','data/taxonomy/names.dmp'))
 				except Exception as e:
-					self.failed.emit('<b><font color="DarkRed">Error loading NCBI names!</font></b><br>Message: <i>'+e.message+'</i>')
+					self.failed.emit('<b><font color="DarkRed">Error loading NCBI names!</font></b><br>Message: <i>'+str(e)+'</i>')
 					raise
 				else:
 					self.done.emit(target)
@@ -1613,7 +1613,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		self.pipelineGui.show()
 				
 	def save_data(self):
-		fname = str(QtGui.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
+		fname = str(QtWidgets.QFileDialog().getSaveFileName(caption='Save Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
 		if len(fname):
 			if not fname.endswith('.gpsa'):
 				if not '.' in fname:
@@ -1631,7 +1631,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 							'settings_analyzer':self.settings_analyzer}
 					pickle.dump(s_data,open(fname,'wb'),protocol=-1)
 				except Exception as e:
-					self.pr('Error while saving file: '+e.message)
+					self.pr('Error while saving file: '+str(e))
 					raise
 				else:
 					self.pr("Finished saving data.")
@@ -1641,7 +1641,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 
 				
 	def load_data(self):
-		dialog = QtGui.QFileDialog(self,'Load Data')
+		dialog = QtWidgets.QFileDialog(self,'Load Data')
 		fname = str(dialog.getOpenFileName(caption='Load Data',filter="GPS Analyzer Files (*.gpsa);;All Files (*.*)",parent=self))
 		if len(fname):
 			self.pr("Loading data from file "+fname)
@@ -1659,7 +1659,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
 					settings_pipeline = settings.get('settings_pipeline',dict())
 					settings_analyzer = settings.get('settings_analyzer',dict())						
 				except Exception as e:
-					self.pr('Error while loading file: '+e.message)
+					self.pr('Error while loading file: '+str(e))
 					raise
 				else:
 					self.treeView.clear()
@@ -1676,17 +1676,17 @@ class GPSAnalyzer(QtGui.QMainWindow):
 		""" Export the whole tree to files that can be loaded with iTOL.
 		http://itol.embl.de/upload.cgi"""
 		try:
-			outdir = str(QtGui.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))
+			outdir = str(QtWidgets.QFileDialog().getExistingDirectory(caption='Select iTOL output directory',parent=self))
 			taxonomy.candidates_to_LCA_tree(self.sgroups,self.taxonomy_nodes,self.taxonomy_names,outdir)
 		except Exception as e:
-			self.pr('Error while saving iTOL files: '+e.message)
+			self.pr('Error while saving iTOL files: '+str(e))
 			raise
 			
 	
 	def export_graphic(self):
 		""" export the current content of the figure to file. Use the DPI 
 		quality specified in exportFigureQuality """
-		dialog = QtGui.QFileDialog(self,'Save Graphic as ...')
+		dialog = QtWidgets.QFileDialog(self,'Save Graphic as ...')
 		fname = str(dialog.getSaveFileName(caption='Save Graphic as ...',filter="Raster Images (*.png *.tiff *.jpg);;Vector Images (*.pdf *.eps)",parent=self))
 		if len(fname) > 0:
 			self.figure.savefig(fname,dpi=self.exportFigureQuality.value())
@@ -1734,7 +1734,7 @@ the LICENSE file shipped with this softw
 		self.treeView.scrollToItem(sel)
 		
 def main():
-	app = QtGui.QApplication(sys.argv)
+	app = QtWidgets.QApplication(sys.argv)
 	GPSAnalyzer() 
 	app.exec_()	
 
--- a/microbegps/modules/composition_analysis.py
+++ b/microbegps/modules/composition_analysis.py
@@ -1,4 +1,4 @@
-from PyQt4 import QtGui
+from PyQt5 import QtGui, QtWidgets
 import matplotlib.pyplot as plt
 
 class GPSModule:
@@ -23,18 +23,18 @@ class GPSModule:
 		self.selectedTaxa = []
 		self.selectedParent = ''
 		
-		self.initialAnalysisLabel = QtGui.QLabel('Initial setup')
+		self.initialAnalysisLabel = QtWidgets.QLabel('Initial setup')
 		self.initialAnalysis = QtGui.QPushButton('Scan GPS results')
 		self.initialAnalysis.setToolTip('Run the initial analysis required for the following steps. This may take some time depending on the amount of data.')
 		self.initialAnalysis.clicked.connect(self.initial_analysis)
 		
-		self.taxRankBoxLabel = QtGui.QLabel('Select a Taxonomic rank')
+		self.taxRankBoxLabel = QtWidgets.QLabel('Select a Taxonomic rank')
 		self.taxRankBox = QtGui.QComboBox()
 		self.taxRankBox.currentIndexChanged.connect(self.select_tax_rank)
-		self.taxGroupBoxLabel = QtGui.QLabel('Select group')
+		self.taxGroupBoxLabel = QtWidgets.QLabel('Select group')
 		self.taxGroupBox = QtGui.QComboBox()
 		self.taxGroupBox.currentIndexChanged.connect(self.select_taxon)
-		self.taxSelectedText = QtGui.QLabel('Found 0 [Not found]')
+		self.taxSelectedText = QtWidgets.QLabel('Found 0 [Not found]')
 		self.getFromTree = QtGui.QPushButton('Get from tree')
 		self.getFromTree.setToolTip('Use the currently selected taxon from the tree.')
 		self.getFromTree.clicked.connect(self.select_taxon_from_tree)
@@ -56,7 +56,7 @@ class GPSModule:
 		tabGrid.addWidget(self.getFromTree, 3,1)
 		tabGrid.addWidget(self.taxSelectedText,4,0)
 		tabGrid.addWidget(self.showComposition,4,1)
-		tabWidget = QtGui.QWidget()
+		tabWidget = QtWidgets.QWidget()
 		tabWidget.setLayout(tabGrid)
 		tabWidget.helpText = self.helpText
 		
--- a/microbegps/modules/export_table.py
+++ b/microbegps/modules/export_table.py
@@ -1,4 +1,4 @@
-from PyQt4 import QtGui
+from PyQt5 import QtGui, QtWidgets
 from os import linesep
 from microbegps import taxonomy
 
@@ -21,7 +21,7 @@ class GPSModule:
 		self.exportSupporting.setToolTip('Also export the supporting genomes of each candidate.')
 		self.exportSupporting.setChecked(False)
 		
-		columnsLabel = QtGui.QLabel('Columns:')
+		columnsLabel = QtWidgets.QLabel('Columns:')
 		
 		self.numReads = QtGui.QCheckBox('Number of Reads')
 		self.numReads.setToolTip('The total number of reads mapped to the candidate/genome.')
@@ -57,7 +57,7 @@ class GPSModule:
 		tabGrid.addWidget(self.genomeValidity,4,1)
 		tabGrid.addWidget(self.homogeneity,5,0)
 		tabGrid.addWidget(self.mappingError,5,1)
-		tabWidget = QtGui.QWidget()
+		tabWidget = QtWidgets.QWidget()
 		tabWidget.setLayout(tabGrid)
 		tabWidget.helpText = self.helpText
 		
--- a/microbegps/modules/search_tab.py
+++ b/microbegps/modules/search_tab.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-from PyQt4 import QtGui
+from PyQt5 import QtGui, QtWidgets
 
 class GPSModule:
 	""" This GPS Module implements a search tab, that allows the user to
@@ -15,7 +15,7 @@ class GPSModule:
 		self.searchText.returnPressed.connect(self.find_reference)
 		self.searchBtn  = QtGui.QPushButton('Find Reference')
 		self.searchBtn.clicked.connect(self.find_reference)
-		self.searchRes  = QtGui.QListWidget()
+		self.searchRes  = QtWidgets.QListWidget()
 		self.searchRes.setMinimumHeight(150)
 		self.searchRes.itemClicked.connect(self.view_search_result)
 		
@@ -24,7 +24,7 @@ class GPSModule:
 		searchGrid.addWidget(self.searchBtn, 0,1)
 		searchGrid.addWidget(self.searchRes, 1,0,1,2)
 		
-		searchWidget = QtGui.QWidget()
+		searchWidget = QtWidgets.QWidget()
 		searchWidget.setLayout(searchGrid)
 		
 		GPS.toolsTab.addTab(searchWidget,"Search")
@@ -38,9 +38,9 @@ class GPSModule:
 		self.searchRes.clear()
 		if len(search_results) > 0:
 			for ref in sorted(search_results):
-				self.searchRes.addItem(QtGui.QListWidgetItem(ref))
+				self.searchRes.addItem(QtWidgets.QListWidgetItem(ref))
 		else:
-			self.searchRes.addItem(QtGui.QListWidgetItem('No matching references found.'))
+			self.searchRes.addItem(QtWidgets.QListWidgetItem('No matching references found.'))
 	
 	def view_search_result(self, item):
 		# View the item selected in the search results in the main window
@@ -54,4 +54,4 @@ class GPSModule:
 		self.GPS.treeView.setCurrentItem(sel)
 		self.GPS.treeView.expand(self.GPS.treeView.currentIndex())
 		self.GPS.treeView.scrollToItem(self.GPS.treeView.currentItem())
-		self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)
\ No newline at end of file
+		self.GPS.tree_item_clicked_handler(self.GPS.treeView.currentItem(),0)
--- a/microbegps/taxonomy.py
+++ b/microbegps/taxonomy.py
@@ -12,7 +12,7 @@ def parse_nodes_dmp(node_file):
 	nodes = dict()
 	ranks = dict()
 	for line in node_file:
-		fields = line.rstrip('\t|\n').split('\t|\t')
+		fields = line.decode('utf-8').rstrip('\t|\n').split('\t|\t')
 		if len(fields) < 4:
 			print('skipped line',line)
 			continue
@@ -28,7 +28,7 @@ def parse_names_dmp(names_file):
 	""" """
 	taxid_to_name = dict()
 	for line in names_file:
-		fields = line.rstrip('\t|\n').split('\t|\t')
+		fields = line.decode('utf-8').rstrip('\t|\n').split('\t|\t')
 		if len(fields) != 4:
 			print('skipped line',line)
 			continue
@@ -45,7 +45,7 @@ def parse_catalog(catalog_file):
 	""" """
 	gi_to_taxid = dict()
 	for line in catalog_file:
-		fields = line.rstrip().split('\t')
+		fields = line.decode('utf-8').rstrip().split('\t')
 		gi = fields[3]
 		taxid = int(fields[0])
 		gi_to_taxid[gi] = taxid
@@ -58,7 +58,7 @@ def gis_to_taxid_and_name(gis, catalog):
 	gi_to_taxid = dict()
 	gi_to_name = dict()
 	for line in catalog:
-		fields = line.rstrip().split('\t')
+		fields = line.decode('utf-8').rstrip().split('\t')
 		gi = fields[3]
 		taxid = int(fields[0])
 		name = fields[1]