class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle("Allele frequency viewer")
self.data = None
self.genes = {}
self.lastopeneddir = os.path.expanduser("~")
self.initUI()
self.init_menu()
self.initRegionViewer()
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.showMaximized()
self.tab_names = []
#self.test()
def test(self) :
vcf = "/Volumes/CORSAIR/PoolsTeo_jan2016/vsYJM326/320_1.rg.dedup.realigned.raw.info.var.vcf"
#vcf = "/media/jevanni/CORSAIR/PoolsTeo_jan2016/vsYJM326/320_1.rg.dedup.realigned.raw.info.var.vcf"
fastafile = "./Anno/yjm326.fasta"
gff3fname = "./Anno/sace_new.gff"
self.load_vcf(vcf)
self.load_annotation(fastafile, gff3fname)
def update_completer_gene(self) :
model = QtGui.QStringListModel()
model.setStringList(self.genes.keys())
self.completer.setModel(model)
def initUI(self) :
self.main_widget = QtGui.QWidget(self)
self.layout = QtGui.QVBoxLayout(self.main_widget)
self.layout_top_right = QtGui.QHBoxLayout()
self.layout_top = QtGui.QHBoxLayout()
# Search bar with auto completer
model = QtGui.QStringListModel()
model.setStringList(self.genes.keys())
self.completer = QtGui.QCompleter()
self.completer.setModel(model)
self.search_bar = QtGui.QLineEdit("Search gene")
self.search_bar.keyPressEvent = self.search_bar_key_event
self.search_bar.mousePressEvent = self.search_bar_mouse_event
self.search_bar.setCompleter(self.completer)
self.af_bar = QtGui.QLineEdit("Set af bar")
self.af_bar.keyPressEvent = self.af_bar_key_event
self.af_bar.mousePressEvent = self.af_bar_mouse_event
self.chromosome_combobox = QtGui.QComboBox()
self.start_bar = QtGui.QLineEdit("Start coordinate")
self.start_bar.keyPressEvent = self.start_bar_key_event
self.start_bar.mousePressEvent = self.start_bar_mouse_event
self.end_bar = QtGui.QLineEdit("End coordinate")
self.end_bar.keyPressEvent = self.end_bar_key_event
self.end_bar.mousePressEvent = self.end_bar_mouse_event
self.layout_top_right.addWidget(self.chromosome_combobox)
self.layout_top_right.addWidget(self.start_bar)
self.layout_top_right.addWidget(self.end_bar)
self.layout_top.addWidget(self.search_bar)
self.layout_top.addWidget(self.af_bar)
self.layout_top.addLayout(self.layout_top_right)
self.tab_widget = QtGui.QTabWidget(self)
self.tab_widget.currentChanged.connect(self.change_tab)
self.statut_bar = QtGui.QStatusBar(self)
self.layout.addLayout(self.layout_top)
self.layout.addWidget(self.tab_widget)
self.layout.addWidget(self.statut_bar)
def init_menu(self) :
self.file_menu = QtGui.QMenu("&Files", self)
self.file_menu.addAction("&Open files", self.load_annotation, QtCore.Qt.CTRL + QtCore.Qt.Key_O)
self.menuBar().addMenu(self.file_menu)
def initRegionViewer(self) :
screen = QtGui.QDesktopWidget()
second_screen = screen.screenGeometry(0)
self.regionViewer = RegionViewer(self)
self.regionViewer.move(second_screen.left(), second_screen.top())
def load_vcf(self, fname=None) :
if not fname : fname = str(QtGui.QFileDialog.getOpenFileName(self, 'Open VCF file', self.lastopeneddir))
if not fname : return False
self.data = DataManager(self, fname)
self.setWindowTitle("Allele frequency viewer : %s" %os.path.basename(fname))
self.chromosome_combobox.addItems(self.data.get_chromosomes())
self.lastopeneddir = os.path.dirname(fname)
self.show_plot()
return True
def load_annotation(self, fasta=None, annofname=None) :
loaded = True
if not self.data : loaded = self.load_vcf()
if not loaded : return
if not fasta : fasta = str(QtGui.QFileDialog.getOpenFileName(self, 'Open Fasta file', self.lastopeneddir))
if not annofname : annofname = str(QtGui.QFileDialog.getOpenFileName(self, 'Open annotation file', self.lastopeneddir))
if not fasta or not annofname : return
self.annotations = get_feature_gff3(annofname, fasta, self.data)
self.genes = self.annotations.get_dict_parents()
self.update_completer_gene()
self.lastopeneddir = os.path.dirname(annofname)
def show_plot(self, chromosome=None) :
name = chromosome if chromosome else "Genome"
if name not in self.tab_names :
canva = self.data.get_canva(chromosome=chromosome)
self.tab_widget.addTab(canva, name)
self.tab_names.append(name)
self.tab_widget.setCurrentIndex(self.tab_names.index(name))
self.get_current_tabwidget().update_info()
def get_current_tabwidget(self) :
return self.tab_widget.currentWidget()
def update_statut_whole(self, chromosome=None) :
info = self.data.get_statut(chromosome=chromosome)
def search_bar_mouse_event(self, event) :
if event.button() == 1 and self.search_bar.text() == "Search gene" :
self.search_bar.setText("")
def search_bar_key_event(self, event) :
if event.text() == '\r' : self.zone_gene(self.search_bar.text())
else : QtGui.QLineEdit.keyPressEvent(self.search_bar, event)
def zone_gene(self, gene_name) :
annotation = self.genes.get(str(gene_name), None)
if not annotation : return
chromosome, start, end = annotation["seqname"], annotation["start"], annotation["end"]
self.show_plot(chromosome=chromosome)
self.get_current_tabwidget().draw_region(start, end)
self.get_current_tabwidget().send_info()
def af_bar_key_event(self, event) :
if event.text() == '\r' : self.set_bar(self.af_bar.text())
else : QtGui.QLineEdit.keyPressEvent(self.af_bar, event)
def af_bar_mouse_event(self, event) :
if event.button() == 1 and self.af_bar.text() == "Set af bar" :
self.af_bar.setText("")
def start_bar_mouse_event(self, event) :
if event.button() == 1 and self.start_bar.text() == "Start coordinate" :
self.start_bar.setText("")
def end_bar_mouse_event(self, event) :
if event.button() == 1 and self.end_bar.text() == "End coordinate" :
self.end_bar.setText("")
def start_bar_key_event(self, event) :
if event.text() == '\r' : self.set_coordinate_manualy()
else : QtGui.QLineEdit.keyPressEvent(self.start_bar, event)
def end_bar_key_event(self, event) :
if event.text() == '\r' : self.set_coordinate_manualy()
else : QtGui.QLineEdit.keyPressEvent(self.end_bar, event)
def set_coordinate_manualy(self) :
chromosome = str(self.chromosome_combobox.currentText())
start = str(self.start_bar.text())
end = str(self.end_bar.text())
try :
start, end = int(start), int(end)
except ValueError :
return
self.show_plot(chromosome=chromosome)
self.get_current_tabwidget().draw_region(start, end)
def set_bar(self, value) :
self.get_current_tabwidget().remove_line()
try : value = float(value)
except ValueError : return
if value > 1 or value < 0 : return
self.get_current_tabwidget().draw_bar(value)
def change_tab(self) :
self.get_current_tabwidget().update_info()
def closeEvent(self, ce) :
if self.regionViewer :
self.regionViewer.close()
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle("Structure Viewer")
self.data_manager = DataManager(self)
self.color_switch = None
self.lastopenfile = None
self.initUI()
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.showMaximized()
self.update_plot()
def initUI(self) :
self.main_widget = QtGui.QWidget(self)
self.main_widget.move(10, 20)
self.main_widget.resize(960, 730)
self.layout = QtGui.QVBoxLayout(self.main_widget)
self.initMenu()
self.error_dialog_load = QtGui.QErrorMessage()
def initMenu(self) :
self.file_menu = QtGui.QMenu("&Options", self)
self.file_menu.addAction("&Open file", self.open_file, QtCore.Qt.CTRL + QtCore.Qt.Key_O)
self.file_menu.addAction("&Save fig", self.save_file, QtCore.Qt.CTRL + QtCore.Qt.Key_S)
self.file_menu.addAction('&Graph settings', self.switch_color, QtCore.Qt.CTRL + QtCore.Qt.Key_G)
self.action_border = QtGui.QAction("Border", self)
self.action_labels = QtGui.QAction("Show all labels", self)
self.action_border.changed.connect(self.update_plot)
self.action_border.setCheckable(True)
self.action_labels.changed.connect(self.update_plot)
self.action_labels.setCheckable(True)
self.file_menu.addAction(self.action_border)
self.file_menu.addAction(self.action_labels)
self.menuBar().addMenu(self.file_menu)
def open_file(self) :
if self.lastopenfile :
fnames = QtGui.QFileDialog.getOpenFileNames(self, 'Open file', dirname(self.lastopenfile))
else :
fnames = QtGui.QFileDialog.getOpenFileNames(self, 'Open file')
for fname in fnames :
try :
self.load_file(fname)
except SVInternalException as error :
self.error_dialog_load.showMessage(str(fname) + " : " + str(error))
return
self.lastopenfile = str(fname)
self.update_plot()
def load_file(self, fname) :
self.data_manager.add_structure_fname(fname)
def update_plot(self) :
# Generate an error, I don't really know why
border = self.is_border_checked()
show_all_labels = self.is_all_labels_checked()
self.canva = self.data_manager.get_canva(edge=border, show_all_labels=show_all_labels)
if not self.canva : return
for i in reversed(range(self.layout.count())):
if isinstance(self.layout.itemAt(i), QtGui.QWidgetItem) :
self.layout.itemAt(i).widget().setParent(None)
self.canva.setParent(self.main_widget)
self.canva.setFocus()
self.layout.addWidget(self.canva)
self.show()
def is_border_checked(self) :
return self.action_border.isChecked()
def is_all_labels_checked(self) :
return self.action_labels.isChecked()
def popup(self, data, row, column) :
self.menu = QtGui.QMenu(self)
go_up_action = QtGui.QAction("Go up", self)
go_up_action.triggered.connect(partial(self.change_row, data, column, 1))
go_down_action = QtGui.QAction("Go down", self)
go_down_action.triggered.connect(partial(self.change_row, data, column, -1))
sort_action = QtGui.QAction("Sort", self)
sort_action.triggered.connect(partial(self.sort_pop, data, column))
self.menu.addAction(go_up_action)
self.menu.addAction(go_down_action)
self.menu.addAction(sort_action)
self.menu.popup(QtGui.QCursor.pos())
def switch_color(self) :
self.color_switch = SwitchColorWindow(self)
def sort_pop(self, data, column) :
data.reorder_pop(column)
self.data_manager.uniform_names(data)
self.update_plot()
def change_row(self, data, column, level) :
if data.reorder_column(column, level) :
self.update_plot()
def save_file(self) :
if self.lastopenfile :
fname = QtGui.QFileDialog.getSaveFileName(self, 'Open file', dirname(self.lastopenfile))
else :
fname = QtGui.QFileDialog.getSaveFileName(self, 'Open file')
self.data_manager.save(str(fname))
def closeEvent(self, ce) :
if self.color_switch :
self.color_switch.terminate()
self.close()
