class ModelFinder(QDialog, Ui_ModelFinder, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
progressSig = pyqtSignal(int) # 控制进度条
startButtonStatusSig = pyqtSignal(list)
logGuiSig = pyqtSignal(str)
search_algorithm = pyqtSignal(str) # 定义所有类都可以使用的信号
workflow_progress = pyqtSignal(int)
workflow_finished = pyqtSignal(str)
iq_tree_exception = pyqtSignal(str) # 定义所有类都可以使用的信号
# 用于flowchart自动popup combobox等操作
showSig = pyqtSignal(QDialog)
closeSig = pyqtSignal(str, str)
# 用于输入文件后判断用
ui_closeSig = pyqtSignal(str)
##弹出识别输入文件的信号
auto_popSig = pyqtSignal(QDialog)
def __init__(
self,
autoMFPath=None,
partFile=None,
workPath=None,
focusSig=None,
IQ_exe=None,
workflow=False,
parent=None):
super(ModelFinder, self).__init__(parent)
self.parent = parent
self.function_name = "ModelFinder"
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
self.modelfinder_exe = '"' + IQ_exe + '"'
self.autoMFPath = autoMFPath[0] if type(autoMFPath) == list else autoMFPath
self.partFile = partFile
self.interrupt = False
self.setupUi(self)
# 保存设置
if not workflow:
self.modelfinder_settings = QSettings(
self.thisPath + '/settings/modelfinder_settings.ini', QSettings.IniFormat)
else:
self.modelfinder_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini', QSettings.IniFormat)
self.modelfinder_settings.beginGroup("Workflow")
self.modelfinder_settings.beginGroup("temporary")
self.modelfinder_settings.beginGroup('ModelFinder')
# File only, no fallback to registry or or.
self.modelfinder_settings.setFallbacksEnabled(False)
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss', encoding="utf-8", errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
# 恢复用户的设置
self.guiRestore()
self.exception_signal.connect(self.popupException)
self.iq_tree_exception.connect(self.popup_IQTREE_exception)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.log_gui = self.gui4Log()
self.lineEdit.installEventFilter(self)
self.lineEdit.autoDetectSig.connect(self.popupAutoDec)
self.lineEdit_2.installEventFilter(self)
self.lineEdit_3.installEventFilter(self)
self.comboBox_3.activated[str].connect(self.controlCodonTable)
self.comboBox_5.activated[str].connect(self.ctrl_ratehet)
self.ctrl_ratehet(self.comboBox_5.currentText())
self.lineEdit_2.setLineEditNoChange(True)
self.lineEdit_3.setLineEditNoChange(True)
self.lineEdit.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
self.lineEdit_2.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
self.lineEdit_3.deleteFile.clicked.connect(
self.clear_lineEdit) # 删除了内容，也要把tooltip删掉
# 初始化codon table的选择
self.controlCodonTable(self.comboBox_3.currentText())
self.checkBox.stateChanged.connect(self.switchPart)
self.switchPart(self.checkBox.isChecked())
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
action = QAction(QIcon(":/picture/resourses/terminal-512.png"), "View | Edit command", menu,
triggered=self.showCMD)
self.work_action = QAction(QIcon(":/picture/resourses/work.png"), "", menu)
self.work_action.triggered.connect(lambda: self.factory.swithWorkPath(self.work_action, parent=self))
self.dir_action = QAction(QIcon(":/picture/resourses/folder.png"), "Output Dir: ", menu)
self.dir_action.triggered.connect(lambda: self.factory.set_direct_dir(self.dir_action, self))
menu.addAction(action)
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True, parent=self) # 初始化一下
## brief demo
self.label_2.clicked.connect(lambda: QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-9-1-Brief-example")))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
try:
self.command = self.getCMD()
if self.command:
self.MF_popen = self.factory.init_popen(self.command)
self.factory.emitCommands(self.logGuiSig, self.command)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
except:
self.exceptionInfo = ''.join(
traceback.format_exception(
*sys.exc_info())) # 捕获报错内容，只能在这里捕获，没有报错的地方无法捕获
self.exception_signal.emit(self.exceptionInfo) # 激发这个信号
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
alignment file
"""
fileName = QFileDialog.getOpenFileName(
self, "Input alignment file", filter="Phylip Format(*.phy *.phylip);;Fasta Format(*.fas *.fasta);;Nexus Format(*.nex *.nexus *.nxs);;Clustal Format(*.aln)")
if fileName[0]:
base = os.path.basename(fileName[0])
self.lineEdit.setText(base)
self.lineEdit.setToolTip(fileName[0])
@pyqtSlot()
def on_pushButton_4_clicked(self):
"""
tree file
"""
fileName = QFileDialog.getOpenFileName(
self, "Input tree file", filter="Newick Format(*.nwk *.newick);;")
if fileName[0]:
base = os.path.basename(fileName[0])
self.lineEdit_2.setText(base)
self.lineEdit_2.setToolTip(fileName[0])
@pyqtSlot()
def on_pushButton_22_clicked(self):
"""
partition file
"""
fileName = QFileDialog.getOpenFileName(
self, "Input partition file", filter="All(*);;")
if fileName[0]:
base = os.path.basename(fileName[0])
self.lineEdit_3.setText(base)
self.lineEdit_3.setToolTip(fileName[0])
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
show log
"""
self.log_gui.show()
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
Stop
"""
if self.isRunning():
if not self.workflow:
reply = QMessageBox.question(
self,
"Confirmation",
"<p style='line-height:25px; height:25px'>ModelFinder is still running, terminate it?</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
else:
reply = QMessageBox.Yes
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
if platform.system().lower() in ["windows", "darwin"]:
self.MF_popen.kill()
else:
os.killpg(os.getpgid(self.MF_popen.pid), signal.SIGTERM)
self.MF_popen = None
self.interrupt = True
except:
self.MF_popen = None
self.interrupt = True
if not self.workflow:
QMessageBox.information(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>Program has been terminated!</p>")
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"except",
self.exportPath,
self.qss_file,
self])
def run_command(self):
try:
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"start",
self.exportPath,
self.qss_file,
self])
self.run_MF()
time_end = datetime.datetime.now()
self.time_used = str(time_end - time_start)
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (str(time_start), str(time_end),
self.time_used)
softWare = self.comboBox_5.currentText()
if softWare in ["BEAST1 (NUC)", "BEAST2 (NUC)", "BEAST (AA)"]:
str1 = self.description + " " + self.parseResults() +\
"\n\nIf you use PhyloSuite, please cite:\nZhang, D., F. Gao, I. Jakovlić, H. Zou, J. Zhang, W.X. Li, and G.T. Wang, PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 2020. 20(1): p. 348–355. DOI: 10.1111/1755-0998.13096.\n" \
"If you use ModelFinder, please cite:\n" + self.reference + \
"\n\nhttps://justinbagley.rbind.io/2016/10/11/setting-dna-substitution-models-beast/\nDetails for setting substitution models in %s\n" % softWare
array = [[i] for i in str1.split(
"\n")] + self.model2beast_des() + [[j] for j in ("\n\n" + self.time_used_des).split("\n")]
self.factory.write_csv_file(
self.exportPath + os.sep + "summary.csv", array, self, silence=True)
else:
with open(self.exportPath + os.sep + "summary.txt", "w", encoding="utf-8") as f:
f.write(self.description + " " + self.parseResults() +
"\n\nIf you use PhyloSuite, please cite:\nZhang, D., F. Gao, I. Jakovlić, H. Zou, J. Zhang, W.X. Li, and G.T. Wang, PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 2020. 20(1): p. 348–355. DOI: 10.1111/1755-0998.13096.\n"
"If you use ModelFinder, please cite:\n" + self.reference + "\n\n" + self.time_used_des)
if not self.interrupt:
if self.workflow:
# work flow跑的
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"workflow stop",
self.exportPath,
self.qss_file,
self])
self.workflow_finished.emit("finished")
return
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"stop",
self.exportPath,
self.qss_file,
self])
else:
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"except",
self.exportPath,
self.qss_file,
self])
if not self.workflow:
self.focusSig.emit(self.exportPath)
except BaseException:
self.exceptionInfo = ''.join(
traceback.format_exception(
*sys.exc_info())) # 捕获报错内容，只能在这里捕获，没有报错的地方无法捕获
self.exception_signal.emit(self.exceptionInfo) # 激发这个信号
self.startButtonStatusSig.emit(
[
self.pushButton,
self.progressBar,
"except",
self.exportPath,
self.qss_file,
self])
def guiSave(self):
# Save geometry
self.modelfinder_settings.setValue('size', self.size())
# self.modelfinder_settings.setValue('pos', self.pos())
for name, obj in inspect.getmembers(self):
# if type(obj) is QComboBox: # this works similar to isinstance, but
# missed some field... not sure why?
if isinstance(obj, QComboBox):
# save combobox selection to registry
index = obj.currentIndex()
self.modelfinder_settings.setValue(name, index)
# if isinstance(obj, QLineEdit):
# text = obj.text()
# tooltip = obj.toolTip()
# self.modelfinder_settings.setValue(name, [text, tooltip])
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.modelfinder_settings.setValue(name, state)
if isinstance(obj, QRadioButton):
state = obj.isChecked()
self.modelfinder_settings.setValue(name, state)
def guiRestore(self):
# Restore geometry
self.resize(self.modelfinder_settings.value('size', QSize(500, 500)))
self.factory.centerWindow(self)
# self.move(self.modelfinder_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox_6":
cpu_num = multiprocessing.cpu_count()
list_cpu = ["AUTO"] + [str(i + 1) for i in range(cpu_num)]
index = self.modelfinder_settings.value(name, "0")
model = obj.model()
obj.clear()
for num, i in enumerate(list_cpu):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
obj.setCurrentIndex(int(index))
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
index = self.modelfinder_settings.value(name, "0")
model = obj.model()
obj.clear()
for num, i in enumerate(allItems):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
obj.setCurrentIndex(int(index))
if isinstance(obj, QLineEdit):
# text, tooltip = self.modelfinder_settings.value(name, ["", ""])
# if os.path.exists(tooltip):
# if os.path.exists(tooltip):
# obj.setText(text)
# obj.setToolTip(tooltip)
if self.autoMFPath and name == "lineEdit":
if os.path.exists(self.autoMFPath):
obj.setText(os.path.basename(self.autoMFPath))
obj.setToolTip(self.autoMFPath)
if self.partFile and name == "lineEdit_3":
self.inputPartition(self.partFile)
if isinstance(obj, QCheckBox):
value = self.modelfinder_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QRadioButton):
value = self.modelfinder_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
def runProgress(self, num):
oldValue = self.progressBar.value()
done_int = int(num)
if done_int > oldValue:
self.progressBar.setProperty("value", done_int)
QCoreApplication.processEvents()
def popupException(self, exception):
print(exception)
rgx = re.compile(r'Permission.+?[\'\"](.+\.csv)[\'\"]')
if rgx.search(exception):
csvfile = rgx.search(exception).group(1)
reply = QMessageBox.critical(
self,
"Extract sequence",
"<p style='line-height:25px; height:25px'>Please close '%s' file first!</p>" % os.path.basename(
csvfile),
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Yes and platform.system().lower() == "windows":
os.startfile(csvfile)
else:
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(
'The program encountered an unforeseen problem, please report the bug at <a href="https://github.com/dongzhang0725/PhyloSuite/issues">https://github.com/dongzhang0725/PhyloSuite/issues</a> or send an email with the detailed traceback to [email protected]')
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def popup_IQTREE_exception(self, text):
if text.endswith("redo"):
reply = QMessageBox.question(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>%s. Do you want to rerun the analysis and overwrite all output files?</p>" % text.replace(
"redo", ""),
QMessageBox.Yes, QMessageBox.No)
if reply == QMessageBox.Yes:
self.interrupt = False
self.run_with_CMD(self.command + " -redo")
else:
QMessageBox.information(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
if "Show log" in text:
self.on_pushButton_9_clicked()
def closeEvent(self, event):
self.guiSave()
self.log_gui.close() # 关闭子窗口
self.closeSig.emit("ModelFinder", self.fetchWorkflowSetting())
# 断开showSig和closeSig的槽函数连接
try:
self.showSig.disconnect()
except:
pass
try:
self.closeSig.disconnect()
except:
pass
if self.workflow:
self.ui_closeSig.emit("ModelFinder")
# 自动跑的时候不杀掉程序
return
if self.isRunning():
# print(self.isRunning())
reply = QMessageBox.question(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>ModelFinder is still running, terminate it?</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
if platform.system().lower() in ["windows", "darwin"]:
self.MF_popen.kill()
else:
os.killpg(os.getpgid(self.MF_popen.pid), signal.SIGTERM)
self.MF_popen = None
self.interrupt = True
except:
self.MF_popen = None
self.interrupt = True
else:
event.ignore()
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
name = obj.objectName()
if isinstance(
obj,
QLineEdit):
if event.type() == QEvent.DragEnter:
if event.mimeData().hasUrls():
# must accept the dragEnterEvent or else the dropEvent
# can't occur !!!
event.accept()
return True
if event.type() == QEvent.Drop:
files = [u.toLocalFile() for u in event.mimeData().urls()]
if name == "lineEdit":
if os.path.splitext(files[0])[1].upper() in [".PHY", ".PHYLIP", ".FAS", ".FASTA", ".NEX", ".NEXUS", ".NXS", ".ALN"]:
base = os.path.basename(files[0])
self.lineEdit.setText(base)
self.lineEdit.setToolTip(files[0])
else:
QMessageBox.information(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>Unsupported file!</p>",
QMessageBox.Ok)
elif name == "lineEdit_2" and os.path.splitext(files[0])[1].upper() in [".NWK", ".NEWICK"]:
base = os.path.basename(files[0])
self.lineEdit_2.setText(base)
self.lineEdit_2.setToolTip(files[0])
elif name == "lineEdit_3":
base = os.path.basename(files[0])
self.lineEdit_3.setText(base)
self.lineEdit_3.setToolTip(files[0])
if (event.type() == QEvent.Show) and (obj == self.pushButton.toolButton.menu()):
if re.search(r"\d+_\d+_\d+\-\d+_\d+_\d+", self.dir_action.text()) or self.dir_action.text() == "Output Dir: ":
self.factory.sync_dir(self.dir_action) ##同步文件夹名字
menu_x_pos = self.pushButton.toolButton.menu().pos().x()
menu_width = self.pushButton.toolButton.menu().size().width()
button_width = self.pushButton.toolButton.size().width()
pos = QPoint(menu_x_pos - menu_width + button_width,
self.pushButton.toolButton.menu().pos().y())
self.pushButton.toolButton.menu().move(pos)
return True
# return QMainWindow.eventFilter(self, obj, event) #
# 其他情况会返回系统默认的事件处理方法。
return super(ModelFinder, self).eventFilter(obj, event) # 0
def gui4Log(self):
dialog = QDialog(self)
dialog.resize(800, 500)
dialog.setWindowTitle("Log")
gridLayout = QGridLayout(dialog)
horizontalLayout_2 = QHBoxLayout()
label = QLabel(dialog)
label.setText("Log of ModelFinder:")
horizontalLayout_2.addWidget(label)
spacerItem = QSpacerItem(
40, 20, QSizePolicy.Expanding, QSizePolicy.Minimum)
horizontalLayout_2.addItem(spacerItem)
toolButton = QToolButton(dialog)
icon2 = QIcon()
icon2.addPixmap(
QPixmap(":/picture/resourses/interface-controls-text-wrap-512.png"))
toolButton.setIcon(icon2)
toolButton.setCheckable(True)
toolButton.setToolTip("Use Wraps")
toolButton.clicked.connect(self.setWordWrap)
toolButton.setChecked(True)
horizontalLayout_2.addWidget(toolButton)
pushButton = QPushButton("Save to file", dialog)
icon = QIcon()
icon.addPixmap(QPixmap(":/picture/resourses/Save-icon.png"))
pushButton.setIcon(icon)
pushButton_2 = QPushButton("Close", dialog)
icon = QIcon()
icon.addPixmap(QPixmap(":/picture/resourses/if_Delete_1493279.png"))
pushButton_2.setIcon(icon)
self.textEdit_log = QTextEdit(dialog)
self.textEdit_log.setReadOnly(True)
gridLayout.addLayout(horizontalLayout_2, 0, 0, 1, 2)
gridLayout.addWidget(self.textEdit_log, 1, 0, 1, 2)
gridLayout.addWidget(pushButton, 2, 0, 1, 1)
gridLayout.addWidget(pushButton_2, 2, 1, 1, 1)
pushButton.clicked.connect(self.save_log_to_file)
pushButton_2.clicked.connect(dialog.close)
dialog.setWindowFlags(
dialog.windowFlags() | Qt.WindowMinMaxButtonsHint)
return dialog
def addText2Log(self, text):
if re.search(r"\w+", text):
self.textEdit_log.append(text)
with open(self.exportPath + os.sep + "PhyloSuite_ModelFinder.log", "a") as f:
f.write(text + "\n")
def save_log_to_file(self):
content = self.textEdit_log.toPlainText()
fileName = QFileDialog.getSaveFileName(
self, "ModelFinder", "log", "text Format(*.txt)")
if fileName[0]:
with open(fileName[0], "w", encoding="utf-8") as f:
f.write(content)
def setWordWrap(self):
button = self.sender()
if button.isChecked():
button.setChecked(True)
self.textEdit_log.setLineWrapMode(QTextEdit.WidgetWidth)
else:
button.setChecked(False)
self.textEdit_log.setLineWrapMode(QTextEdit.NoWrap)
def isRunning(self):
'''判断程序是否运行,依赖进程是否存在来判断'''
return hasattr(self, "MF_popen") and self.MF_popen and not self.interrupt
def controlCodonTable(self, text):
if text in ["Codon", "DNA-->AA"]:
self.comboBox_9.setEnabled(True)
else:
self.comboBox_9.setEnabled(False)
if text == "Codon":
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>If you choose \"Codon\" sequence type, "
"only \"IQ-TREE\" is allowed as the \"Model for\" option!</p>")
self.comboBox_5.setCurrentText("IQ-TREE")
def run_MF(self):
rgx_test_model = re.compile(r"^ModelFinder will test (\d+) \w+ models")
rgx_part_model = re.compile(r"^Loading (\d+) partitions\.\.\.")
rgx_finished = re.compile(r"^Date and Time:")
self.totleModels = None
self.totlePartitions_2 = None
list_partition_names = [] # 存放partition的名字
num = 0 # partition出现的次数，当num等于2倍partition的个数的时候，就完成
is_error = False ##判断是否出了error
while True:
QApplication.processEvents()
if self.isRunning():
try:
out_line = self.MF_popen.stdout.readline().decode("utf-8", errors="ignore")
except UnicodeDecodeError:
out_line = self.MF_popen.stdout.readline().decode("gbk", errors="ignore")
if out_line == "" and self.MF_popen.poll() is not None:
break
list_outline = out_line.strip().split()
if rgx_test_model.search(out_line):
self.totleModels = int(
rgx_test_model.search(out_line).group(1))
self.progressSig.emit(5)
self.workflow_progress.emit(5)
elif rgx_part_model.search(out_line):
self.totlePartitions_2 = 2 * \
int(rgx_part_model.search(out_line).group(1))
self.progressSig.emit(5)
self.workflow_progress.emit(5)
elif self.totleModels and (len(list_outline) == 7) and list_outline[0].isdigit() and list_outline[3].isdigit():
# 普通模式
model_num = int(list_outline[0])
self.progressSig.emit(
5 + model_num * 90 / self.totleModels)
self.workflow_progress.emit(
5 + model_num * 90 / self.totleModels)
# 下面2个是partition mode
elif self.totlePartitions_2 and re.search(r"^\d", out_line) and len(out_line.strip().split("\t")) == 8:
# partition模式, Subset Type Seqs Sites Infor
# Invar Model Name
list_partition_names.append(
out_line.strip().split("\t")[-1])
elif list_partition_names and self.totlePartitions_2 and (num <= self.totlePartitions_2) and re.search(r"^ +\d+|^Optimizing", out_line):
for i in list_partition_names:
if i in out_line:
num += 1
self.progressSig.emit(
5 + num * 90 / self.totlePartitions_2)
self.workflow_progress.emit(
5 + num * 90 / self.totlePartitions_2)
# print(num, self.totlePartitions_2)
elif rgx_finished.search(out_line):
self.progressSig.emit(100)
self.workflow_progress.emit(100)
text = out_line.strip() if re.search(r"\w", out_line) else "\n"
self.logGuiSig.emit(text)
if re.search(r"^ERROR", out_line):
is_error = True
# self.on_pushButton_9_clicked()
# redo
if re.search(r"(?m)(^Checkpoint.+?a previous run successfully finished)", out_line):
self.interrupt = True
text = re.search(
r"(?m)(^Checkpoint.+?a previous run successfully finished)", out_line).group(1)
self.iq_tree_exception.emit(text + "redo")
else:
break
if is_error:
self.interrupt = True
self.iq_tree_exception.emit(
"Error happened! Click <span style='font-weight:600; color:#ff0000;'>Show log</span> to see detail!")
self.MF_popen = None
def clear_lineEdit(self):
sender = self.sender()
lineEdit = sender.parent()
lineEdit.setText("")
lineEdit.setToolTip("")
def ctrl_ratehet(self, text):
if text == "IQ-TREE":
self.checkBox_2.setEnabled(True)
else:
self.checkBox_2.setEnabled(False)
if self.comboBox_3.currentText() == "Codon" and text != "IQ-TREE":
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>If you choose \"Codon\" sequence type, "
"only \"IQ-TREE\" is allowed as the \"Model for\" option!</p>")
self.comboBox_5.setCurrentText("IQ-TREE")
def workflow_input(self, MSA=None, partition=None):
self.lineEdit.setText("")
self.lineEdit_2.setText("")
self.lineEdit_3.setText("")
if MSA:
MSA = MSA[0] if type(MSA) == list else MSA
self.lineEdit.setText(os.path.basename(MSA))
self.lineEdit.setToolTip(MSA)
if partition:
self.inputPartition(partition)
def inputPartition(self, partition):
if os.path.exists(partition):
with open(partition, encoding="utf-8", errors='ignore') as f:
partition_txt = f.read()
iq_partition = re.search(
r"(?s)\*\*\*IQ-TREE style\*\*\*(.+?)[\*|$]", partition_txt).group(1).strip()
path = os.path.dirname(partition) + os.sep + "MF_partition.txt"
with open(path, "w", encoding="utf-8") as f1:
f1.write(iq_partition)
self.lineEdit_3.setText(os.path.basename(path))
self.lineEdit_3.setToolTip(path)
def popupAutoDec(self, init=False):
self.init = init
self.factory.popUpAutoDetect(
"ModelFinder", self.workPath, self.auto_popSig, self)
def popupAutoDecSub(self, popupUI):
if not popupUI:
if not self.init:
QMessageBox.warning(
self,
"Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>")
return
if not self.init: popupUI.checkBox.setVisible(False)
if popupUI.exec_() == QDialog.Accepted:
widget = popupUI.listWidget_framless.itemWidget(
popupUI.listWidget_framless.selectedItems()[0])
input_file, partition_file = widget.autoInputs
self.workflow_input(input_file, partition_file)
def fetchWorkflowSetting(self):
'''* if partition mode, partition style:
* seq type:
* code table(if codon)
* criterion
* model for: '''
settings = '''<p class="title">***ModelFinder***</p>'''
ifPartition = "Yes" if self.checkBox.isChecked() else "No"
settings += '<p>Partition mode: <a href="self.ModelFinder_exe' \
' factory.highlightWidgets(x.checkBox)">%s</a></p>' % ifPartition
if ifPartition == "Yes":
partStyle = "Edge-linked" if self.radioButton.isChecked() else "Edge-unlinked"
settings += '<p>Partition style: <a href="self.ModelFinder_exe' \
' factory.highlightWidgets(x.radioButton,x.radioButton_2)">%s</a></p>' % partStyle
seq_type = self.comboBox_3.currentText()
settings += '<p>Sequence type: <a href="self.ModelFinder_exe comboBox_3.showPopup()' \
' factory.highlightWidgets(x.comboBox_3)">%s</a></p>' % seq_type
threads = self.comboBox_6.currentText()
settings += '<p>Threads: <a href="self.ModelFinder_exe comboBox_6.showPopup()' \
' factory.highlightWidgets(x.comboBox_6)">%s</a></p>' % threads
if seq_type == "Codon":
code_table = self.comboBox_9.currentText()
settings += '<p>Code table: <a href="self.ModelFinder_exe comboBox_9.showPopup()' \
' factory.highlightWidgets(x.comboBox_9)">%s</a></p>' % code_table
criterion = self.comboBox_4.currentText()
settings += '<p>Criterion: <a href="self.ModelFinder_exe comboBox_4.showPopup()' \
' factory.highlightWidgets(x.comboBox_4)">%s</a></p>' % criterion
modelFor = self.comboBox_5.currentText()
settings += '<p>Model used for: <a href="self.ModelFinder_exe comboBox_5.showPopup()' \
' factory.highlightWidgets(x.comboBox_5)">%s</a></p>' % modelFor
return settings
def showEvent(self, event):
QTimer.singleShot(100, lambda: self.showSig.emit(self))
# self.showSig.emit(self)
def isFileIn(self):
alignment = self.lineEdit.toolTip()
if os.path.exists(alignment):
return alignment
else:
return False
def parseResults(self):
# 非partition模式
list_input_model_file = [self.exportPath + os.sep + i for i in os.listdir(self.exportPath) if
os.path.splitext(i)[1].upper() == ".IQTREE"]
input_model_file = list_input_model_file[
0] if list_input_model_file else ""
if input_model_file:
f = self.factory.read_file(input_model_file)
# with open(input_model_file, encoding="utf-8", errors='ignore') as f: #"rb",
model_content = f.read()
# f.close()
rgx_model = re.compile(r"(Best-fit model according to.+?\: )(.+)")
# softWare = self.comboBox_5.currentText()
# if softWare in ["BEAST1", "BEAST2"]:
# prefix = rgx_model.search(model_content).group(1)
# model = rgx_model.search(model_content).group(2)
# version = softWare[-1]
# model_split = model.split("+")[0]
# model4beast, addSpecify = self.convertModel2beast(softWare, model_split)
# best_model = model.replace(model_split, model4beast)
# best_model = prefix + best_model + " [Additional specifications in BEAUti%s: %s]"%(version, addSpecify) \
# if addSpecify else prefix + best_model
# else:
best_model = rgx_model.search(model_content).group()
else:
best_model = ""
return best_model + "."
# def convertModel2beast(self, softWare, model):
# '''作废'''
# if softWare == "BEAST1":
# model_replace = {"JC69": ["JC69", ""],
# "TrN": ["TN93", ""],
# "TrNef": ["TN93", 'base Frequencies set to "All Equal"'],
# "K80": ["HKY", 'base Frequencies set to "All Equal"'],
# "K2P": ["HKY", 'base Frequencies set to "All Equal"'],
# "F81": ["GTR", 'turn off operators for all rate parameters'],
# "HKY": ["HKY", ''],
# "SYM": ["GTR", 'base Frequencies set to "All Equal"'],
# "TIM": ["GTR", 'edit XML file by hand so that all other rates are equal to the AG rate'],
# "TVM": ["GTR", 'unchecking AG rate operator'],
# "TVMef": ["GTR", 'unchecking AG rate operator and setting base Frequencies to "All Equal"'],
# "GTR": ["GTR", '']}
# if model in model_replace:
# return model_replace[model]
# else:
# return [model, '']
# else:
# #BEAST2
# model_replace = {"JC69": ["JC69", ""],
# "TrN": ["TN93", ""],
# "TrNef": ["TN93", 'base Frequencies set to "All Equal"'],
# "K80": ["HKY", 'base Frequencies set to "All Equal"'],
# "K2P": ["HKY", 'base Frequencies set to "All Equal"'],
# "F81": ["GTR", 'fix all rate parameters to 1.0 (uncheck the "estimate" box)'],
# "HKY": ["HKY", ''],
# "SYM": ["GTR", 'base Frequencies set to "All Equal"'],
# "TIM": ["GTR", 'fix CT and AG rate parameters to 1.0 (uncheck the "estimate" box)'],
# "TVM": ["GTR", 'fix the AG rate parameter to 1.0 (uncheck the "estimate" box)'],
# "TVMef": ["GTR", 'fix the AG rate parameter to 1.0 (uncheck the "estimate" box), '
# 'and also set base Frequencies to "All Equal"'],
# "GTR": ["GTR", '']}
# if model in model_replace:
# return model_replace[model]
# else:
# return [model, '']
def model2beast_des(self):
softWare = self.comboBox_5.currentText()
if softWare == "BEAST1 (NUC)":
return [['Best-fit substitution model', '(Base) Model to select in BEAUti', 'Additional specifications in BEAUti'],
['JC69', 'JC69', 'None '],
['TrN', 'TN93', 'None '],
['TrNef', 'TN93', 'base Frequencies set to "All Equal"'],
['K80 (K2P)', 'HKY',
'base Frequencies set to "All Equal"'],
['F81', 'GTR',
'turn off operators for all rate parameters'],
['HKY', 'HKY', 'None'],
['SYM', 'GTR', 'base Frequencies set to "All Equal"'],
['TIM', 'GTR',
'edit XML file by hand so that all other rates are equal to the AG rate'],
['TVM', 'GTR', 'unchecking AG rate operator'],
['TVMef', 'GTR',
'unchecking AG rate operator and setting base Frequencies to "All Equal"'],
['GTR', 'GTR', 'None']]
elif softWare == "BEAST2 (NUC)":
return [['Best-fit substitution model', '(Base) Model to select in BEAUti 2', 'Additional specifications in BEAUti 2'],
['JC69', 'JC69', 'None '],
['TrN', 'TN93', 'None'],
['TrNef', 'TN93', 'base Frequencies set to "All Equal"'],
['K80 (K2P)', 'HKY',
'base Frequencies set to "All Equal"'],
['F81', 'GTR',
'fix all rate parameters to 1.0 (uncheck the "estimate" box)'],
['HKY', 'HKY', ' None'],
['SYM', 'GTR', 'base Frequencies set to "All Equal"'],
['TIM', 'GTR',
'fix CT and AG rate parameters to 1.0 (uncheck the "estimate" box)'],
['TVM', 'GTR',
'fix the AG rate parameter to 1.0 (uncheck the "estimate" box)'],
['TVMef', 'GTR',
'fix the AG rate parameter to 1.0 (uncheck the "estimate" box), and also set base Frequencies to "All Equal"'],
['GTR', 'GTR', ' None']]
else:
return []
def switchPart(self, state):
if state:
if not self.workflow:
self.lineEdit_3.setEnabled(True)
self.pushButton_22.setEnabled(True)
else:
if not self.workflow:
self.lineEdit_3.setEnabled(False)
self.pushButton_22.setEnabled(False)
def getCMD(self):
alignment = self.isFileIn()
if alignment:
# 有数据才执行
self.output_dir_name = self.factory.fetch_output_dir_name(self.dir_action)
self.interrupt = False
self.exportPath = self.factory.creat_dirs(self.workPath +
os.sep + "ModelFinder_results" + os.sep + self.output_dir_name)
ok = self.factory.remove_dir(self.exportPath, parent=self)
if not ok:
# 提醒是否删除旧结果，如果用户取消，就不执行
return
os.chdir(self.exportPath) # 因为用了-pre，所以要先切换目录到该文件夹
inputFile = os.path.basename(
shutil.copy(alignment, self.exportPath))
pre = " -pre \"%s\""%self.factory.refineName(inputFile + "." + self.comboBox_5.currentText().lower().replace("-", "_"))
# use_model_for = " -m MF" if self.comboBox_5.currentText() == "IQ-TREE" else " -m TESTONLY -mset %s"%self.comboBox_5.currentText().lower()
if self.comboBox_5.currentText() == "IQ-TREE":
if self.checkBox_2.isChecked():
print(self.lineEdit_3.toolTip())
if self.checkBox.isChecked() and self.lineEdit_3.toolTip() and self.lineEdit_3.isEnabled(): # partition
#确保勾选了partition以及输入了文件
use_model_for = " -m TESTNEWMERGEONLY"
else:
use_model_for = " -m TESTNEWONLY"
else:
if self.checkBox.isChecked() and self.lineEdit_3.toolTip() and self.lineEdit_3.isEnabled(): # partition
use_model_for = " -m TESTMERGEONLY"
else:
use_model_for = " -m TESTONLY"
elif self.comboBox_5.currentText() in ["BEAST1 (NUC)", "BEAST2 (NUC)"]:
use_model_for = " -mset JC69,TrN,TrNef,K80,K2P,F81,HKY,SYM,TIM,TVM,TVMef,GTR -mrate E,G"
elif self.comboBox_5.currentText() in ["BEAST (AA)"]:
use_model_for = " -mset Blosum62,cpREV,JTT,mtREV,WAG,LG,Dayhoff -mrate E,G"
else:
use_model_for = " -m TESTONLY -mset %s" % self.comboBox_5.currentText().lower() \
if ((not self.checkBox.isChecked()) or (not self.lineEdit_3.toolTip())) else " -m TESTMERGEONLY -mset %s" % self.comboBox_5.currentText().lower()
criterion_org = re.search(
r"\((\w+)\)", self.comboBox_4.currentText()).group(1)
criterion = " -%s" % criterion_org if criterion_org != "BIC" else ""
dict_seq = {"DNA": "DNA", "Protein": "AA", "Codon": "CODON", "Binary": "BIN", "Morphology": "MORPH",
"DNA-->AA": "NT2AA"}
seqType = " -st %s" % dict_seq[
self.comboBox_3.currentText()] if self.comboBox_3.currentText() != "Auto detect" else ""
codon_table_index = self.comboBox_9.currentText().split(" ")[0]
seqType = seqType + \
codon_table_index if seqType in [
" -st CODON", " -st NT2AA"] else seqType
treeFile = " -te %s" % shutil.copy(self.lineEdit_2.toolTip(),
self.exportPath) if self.lineEdit_2.toolTip() else ""
partitionCMD = "-spp" if self.radioButton.isChecked() else "-sp"
partFile = " %s \"%s\"" % (
partitionCMD, os.path.basename(shutil.copy(self.lineEdit_3.toolTip(), self.exportPath))) if (
self.checkBox.isChecked() and self.lineEdit_3.toolTip()) else ""
threads = " -nt %s" % self.comboBox_6.currentText()
command = self.modelfinder_exe + " -s \"%s\"" % inputFile + \
use_model_for + criterion + seqType + \
treeFile + partFile + threads + pre
# print(self.command)
self.textEdit_log.clear() # 清空
# 描述
type = "Edge-linked" if self.radioButton.isChecked() else "Edge-unlinked"
model = "best-fit model" if not partFile else "best-fit partition model (%s)" % type
self.description = '''ModelFinder (Kalyaanamoorthy et al., 2017) was used to select the %s using %s criterion.''' % (
model, criterion_org)
self.reference = "Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., von Haeseler, A., Jermiin, L.S., 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587-589."
return command
else:
QMessageBox.critical(
self,
"ModelFinder",
"<p style='line-height:25px; height:25px'>Please input alignment file first!</p>")
return None
def showCMD(self):
"""
show command
"""
self.command = self.getCMD()
if self.command:
dialog = QDialog(self)
dialog.resize(600, 200)
dialog.setWindowTitle("Command")
gridLayout = QGridLayout(dialog)
label = QLabel(dialog)
label.setText("Current Command:")
pushButton = QPushButton("Save and run", dialog)
icon = QIcon()
icon.addPixmap(QPixmap(":/picture/resourses/Save-icon.png"))
pushButton.setIcon(icon)
pushButton_2 = QPushButton("Close", dialog)
icon = QIcon()
icon.addPixmap(
QPixmap(":/picture/resourses/if_Delete_1493279.png"))
pushButton_2.setIcon(icon)
self.textEdit_cmd = QTextEdit(dialog)
self.textEdit_cmd.setText(self.command)
gridLayout.addWidget(label, 0, 0, 1, 2)
gridLayout.addWidget(self.textEdit_cmd, 1, 0, 1, 2)
gridLayout.addWidget(pushButton, 2, 0, 1, 1)
gridLayout.addWidget(pushButton_2, 2, 1, 1, 1)
pushButton.clicked.connect(
lambda: [self.run_with_CMD(self.textEdit_cmd.toPlainText()), dialog.close()])
pushButton_2.clicked.connect(dialog.close)
dialog.setWindowFlags(
dialog.windowFlags() | Qt.WindowMinMaxButtonsHint)
dialog.exec_()
def run_with_CMD(self, cmd):
self.command = cmd
if self.command:
self.MF_popen = self.factory.init_popen(self.command)
self.factory.emitCommands(self.logGuiSig, self.command)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
class Gblocks(QDialog, Ui_Gblocks, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
progressSig = pyqtSignal(int) # 控制进度条
startButtonStatusSig = pyqtSignal(list)
logGuiSig = pyqtSignal(str)
workflow_progress = pyqtSignal(int)
workflow_finished = pyqtSignal(str)
auto_parSig = pyqtSignal()
gblocks_exception = pyqtSignal(str) # 定义所有类都可以使用的信号
# 用于flowchart自动popup combobox等操作
showSig = pyqtSignal(QDialog)
closeSig = pyqtSignal(str, str)
# 用于输入文件后判断用
ui_closeSig = pyqtSignal(str)
##弹出识别输入文件的信号
auto_popSig = pyqtSignal(QDialog)
def __init__(self,
autoInputs=None,
workPath=None,
focusSig=None,
gb_exe=None,
workflow=False,
parent=None):
super(Gblocks, self).__init__(parent)
self.parent = parent
self.function_name = "Gblocks"
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
self.gb_exe = '"' + gb_exe + '"'
self.autoInputs = autoInputs
self.interrupt = False
self.setupUi(self)
# 保存设置
if not workflow:
self.gblocks_settings = QSettings(
self.thisPath + '/settings/gblocks_settings.ini',
QSettings.IniFormat)
else:
self.gblocks_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.gblocks_settings.beginGroup("Workflow")
self.gblocks_settings.beginGroup("temporary")
self.gblocks_settings.beginGroup('Gblocks')
# File only, no fallback to registry or or.
self.gblocks_settings.setFallbacksEnabled(False)
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss',
encoding="utf-8",
errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
# 恢复用户的设置
self.guiRestore()
self.log_gui = self.gui4Log()
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.gblocks_exception.connect(self.popup_Gblocks_exception)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
# self.comboBox_4.itemRemovedSig.connect(self.auto_parFromfile)
self.comboBox_2.currentIndexChanged[str].connect(self.comboLink)
reg_ex = QRegExp(".{,5}")
validator = QRegExpValidator(reg_ex, self.lineEdit_3)
self.lineEdit_3.setValidator(validator)
self.auto_parSig.connect(self.auto_parFromfile)
# 给开始按钮添加菜单
menu = QMenu(self)
menu.setToolTipsVisible(True)
self.work_action = QAction(QIcon(":/picture/resourses/work.png"), "",
menu)
self.work_action.triggered.connect(
lambda: self.factory.swithWorkPath(self.work_action, parent=self))
self.dir_action = QAction(QIcon(":/picture/resourses/folder.png"),
"Output Dir: ", menu)
self.dir_action.triggered.connect(
lambda: self.factory.set_direct_dir(self.dir_action, self))
menu.addAction(self.work_action)
menu.addAction(self.dir_action)
self.pushButton.toolButton.setMenu(menu)
self.pushButton.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True,
parent=self) # 初始化一下
## brief demo
self.label_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-6-1-Brief-example"
)))
##自动弹出识别文件窗口
self.auto_popSig.connect(self.popupAutoDecSub)
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
if self.isFileIn():
# 创建输出文件夹
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + os.sep +
"Gblocks_results" +
os.sep +
self.output_dir_name)
self.interrupt = False
ok = self.factory.remove_dir(self.exportPath,
parent=self) # 第二次运行的时候要清空
if not ok:
# 提醒是否删除旧结果，如果用户取消，就不执行
return
self.collect_args()
self.textEdit_log.clear() # 清空log
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.critical(
self, "Gblocks",
"<p style='line-height:25px; height:25px'>Please input files first!</p>"
)
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
open files
"""
fileNames = QFileDialog.getOpenFileNames(
self,
"Input Files",
filter="NBRF/PIR Format(*.pir);;Fasta Format(*.fas *.fasta *.fsa);;"
)
if fileNames[0]:
self.input(fileNames[0])
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
show log
"""
self.log_gui.show()
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
Stop
"""
if self.isRunning():
if not self.workflow:
reply = QMessageBox.question(
self, "Confirmation",
"<p style='line-height:25px; height:25px'>Gblocks is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
else:
reply = QMessageBox.Yes
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
if platform.system().lower() in ["windows", "darwin"]:
self.gb_popen.kill()
else:
os.killpg(os.getpgid(self.gb_popen.pid),
signal.SIGTERM)
self.gb_popen = None
self.interrupt = True
except:
self.gb_popen = None
self.interrupt = True
if not self.workflow:
QMessageBox.information(
self, "Gblocks",
"<p style='line-height:25px; height:25px'>Program has been terminated!</p>"
)
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.exportPath, self.qss_file, self
])
def run_command(self):
try:
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start", self.exportPath,
self.qss_file, self
])
# if not self.workflow:
self.input_files = []
for j in self.files:
shutil.copy(j, self.exportPath)
self.input_files.append(os.path.basename(j))
os.chdir(self.exportPath)
# self.input_files = os.listdir(self.exportPath)
for num, self.input_file in enumerate(self.input_files):
if self.seq_num_differ and (self.workflow or self.runAnyway):
with open(self.input_file,
encoding="utf-8",
errors='ignore') as f:
content = f.read()
self.seq_num = content.count(">")
self.auto_parFromfile()
# self.auto_parSig.emit()
self.collect_args() # 参数刷新了
commands = "{self.gb_exe} \"{self.input_file}\" -t={self.t} -b1={self.b1} -b2={self.b2} -b3={self.b3} -b4={self.b4} -b5={self.b5}{self.b6} -s={self.s} -p={self.p} -v={self.v} -n={self.n} -u={self.u} -k={self.k} -d={self.d} -e={self.e}".format(
self=self)
# print(os.path.basename(self.input_file), commands)
self.run_code(commands)
self.progressSig.emit((num + 1) * 100 / len(self.input_files))
self.workflow_progress.emit(
(num + 1) * 100 / len(self.input_files))
if self.interrupt:
return
# 将gb后缀放到前面
for j in os.listdir(self.exportPath):
name, ext = os.path.splitext(j)
if ext.endswith(self.e):
# 将ext的后缀放到前面
if not os.path.exists(self.exportPath + os.sep + name +
self.e + ".fasta"):
os.rename(
self.exportPath + os.sep + j, self.exportPath +
os.sep + name + self.e + ".fasta")
else:
try:
os.remove(self.exportPath + os.sep + j)
except:
pass
if self.interrupt:
break
time_end = datetime.datetime.now()
self.time_used = str(time_end - time_start)
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (
str(time_start), str(time_end), self.time_used)
with open(self.exportPath + os.sep + "summary.txt",
"w",
encoding="utf-8") as f:
f.write(
self.description +
"\n\nIf you use PhyloSuite, please cite:\nZhang, D., F. Gao, I. Jakovlić, H. Zou, J. Zhang, W.X. Li, and G.T. Wang, PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources, 2020. 20(1): p. 348–355. DOI: 10.1111/1755-0998.13096.\n"
"If you use Gblocks, please cite:\n" + self.reference +
"\n\n" + self.time_used_des)
if not self.interrupt:
if self.workflow:
# work flow跑的
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "workflow stop",
self.exportPath, self.qss_file, self
])
self.workflow_finished.emit("finished")
return
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "stop", self.exportPath,
self.qss_file, self
])
self.focusSig.emit(self.exportPath)
else:
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.exportPath, self.qss_file, self
])
except BaseException:
self.exceptionInfo = ''.join(
traceback.format_exception(
*sys.exc_info())) # 捕获报错内容，只能在这里捕获，没有报错的地方无法捕获
self.exception_signal.emit(self.exceptionInfo) # 激发这个信号
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except", self.exportPath,
self.qss_file, self
])
def guiSave(self):
# Save geometry
self.gblocks_settings.setValue('size', self.size())
# self.gblocks_settings.setValue('pos', self.pos())
for name, obj in inspect.getmembers(self):
# if type(obj) is QComboBox: # this works similar to isinstance, but
# missed some field... not sure why?
if isinstance(obj, QComboBox):
# save combobox selection to registry
if name != "comboBox_4":
text = obj.currentText()
if text:
allItems = [
obj.itemText(i) for i in range(obj.count())
]
allItems.remove(text)
sortItems = [text] + allItems
self.gblocks_settings.setValue(name, sortItems)
if isinstance(obj, QRadioButton):
state = obj.isChecked()
self.gblocks_settings.setValue(name, state)
if isinstance(obj, QLineEdit):
text = obj.text()
self.gblocks_settings.setValue(name, text)
if isinstance(obj, QSpinBox):
value = obj.value()
self.gblocks_settings.setValue(name, value)
def guiRestore(self):
# Restore geometry
self.resize(self.gblocks_settings.value('size', QSize(658, 500)))
self.factory.centerWindow(self)
# self.move(self.gblocks_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name not in ["comboBox_10", "comboBox_2"]:
allItems = [obj.itemText(i) for i in range(obj.count())]
values = self.gblocks_settings.value(name, allItems)
if name == "comboBox_4":
if not self.workflow:
if self.autoInputs:
self.input(self.autoInputs)
else:
self.input(values)
else:
self.input([])
else:
model = obj.model()
obj.clear()
for num, i in enumerate(values):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
if isinstance(obj, QRadioButton):
value = self.gblocks_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QLineEdit):
value = self.gblocks_settings.value(
name, "_gb") # get stored value from registry
obj.setText(value)
if isinstance(obj, QSpinBox):
value = self.gblocks_settings.value(
name) # get stored value from registry
if value:
obj.setValue(int(value))
if self.radioButton_2.isChecked():
self.comboBox_13.setEnabled(True)
elif self.radioButton.isChecked() or self.radioButton_3.isChecked():
self.comboBox_13.setEnabled(False)
def runProgress(self, num):
oldValue = self.progressBar.value()
done_int = int(num)
if done_int > oldValue:
self.progressBar.setProperty("value", done_int)
QCoreApplication.processEvents()
def popupException(self, exception):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(
'The program encountered an unforeseen problem, please report the bug at <a href="https://github.com/dongzhang0725/PhyloSuite/issues">https://github.com/dongzhang0725/PhyloSuite/issues</a> or send an email with the detailed traceback to [email protected]'
)
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def closeEvent(self, event):
self.guiSave()
self.log_gui.close() # 关闭子窗口
self.closeSig.emit("Gblocks", self.fetchWorkflowSetting())
# 取消选中文字
self.radioButton.setFocus()
self.spinBox_2.lineEdit().deselect()
self.spinBox_3.lineEdit().deselect()
# 断开showSig和closeSig的槽函数连接
try:
self.showSig.disconnect()
except:
pass
try:
self.closeSig.disconnect()
except:
pass
if self.workflow:
self.ui_closeSig.emit("Gblocks")
# 自动跑的时候不杀掉程序
return
if self.isRunning():
# print(self.isRunning())
reply = QMessageBox.question(
self, "Gblocks",
"<p style='line-height:25px; height:25px'>Gblocks is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
if platform.system().lower() in ["windows", "darwin"]:
self.gb_popen.kill()
else:
os.killpg(os.getpgid(self.gb_popen.pid),
signal.SIGTERM)
self.gb_popen = None
self.interrupt = True
except:
self.gb_popen = None
self.interrupt = True
else:
event.ignore()
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
if isinstance(obj, QComboBox):
if event.type() == QEvent.DragEnter:
if event.mimeData().hasUrls():
# must accept the dragEnterEvent or else the dropEvent
# can't occur !!!
event.accept()
return True
if event.type() == QEvent.Drop:
files = [u.toLocalFile() for u in event.mimeData().urls()]
pick_files = [
i for i in files if os.path.splitext(i)[1].upper() in
[".FASTA", ".FAS", ".PIR", ".NBRF"]
]
if pick_files:
self.input(files)
else:
QMessageBox.warning(
self, "Gblocks",
"<p style='line-height:25px; height:25px'>Only files in fasta, nbrf and pir formats are allowed!</p>"
)
if (event.type()
== QEvent.Show) and (obj == self.pushButton.toolButton.menu()):
if re.search(r"\d+_\d+_\d+\-\d+_\d+_\d+", self.dir_action.text()
) or self.dir_action.text() == "Output Dir: ":
self.factory.sync_dir(self.dir_action) ##同步文件夹名字
menu_x_pos = self.pushButton.toolButton.menu().pos().x()
menu_width = self.pushButton.toolButton.menu().size().width()
button_width = self.pushButton.toolButton.size().width()
pos = QPoint(menu_x_pos - menu_width + button_width,
self.pushButton.toolButton.menu().pos().y())
self.pushButton.toolButton.menu().move(pos)
return True
return super(Gblocks, self).eventFilter(obj, event) # 0
def input(self, infiles):
self.comboBox_4.refreshInputs([]) # 先刷新一个空的
dict_taxon_num = {}
self.seq_num_differ = False # 序列数目相同就是false
self.runAnyway = False
self.comboBox_10.setDisabled(False)
self.comboBox_2.setDisabled(False)
new_infiles = [] # 预防有时候有些文件无效
for i in infiles:
if not os.path.exists(i):
continue
with open(i, encoding="utf-8", errors='ignore') as f:
content = f.read()
self.seq_num = content.count(">")
if self.seq_num == 0:
self.popup_Gblocks_exception(
"The file %s is not in fasta format!" %
(os.path.basename(i)))
self.comboBox_4.refreshInputs([])
return
try:
if re.search(r"(?m)^\n(?!\>)", content):
# 序列内部有空行
content = re.sub(r"(?m)^\n(?!\>)", "", content)
with open(i, "w", encoding="utf-8") as f1:
# 重新保存一下该文件
f1.write(content)
else:
# 多了一个\r的情况
with open(i, "w", encoding="utf-8") as f1:
# 重新保存一下该文件
f1.write(content)
except:
pass
dict_taxon_num.setdefault(self.seq_num,
[]).append(os.path.basename(i))
new_infiles.append(i)
if not new_infiles: # 如果没有有效的文件
return
if len(dict_taxon_num) > 1:
self.seq_num_differ = True
# 物种数目一样,如果是workflow方式，就直接都用最低配置
if len(dict_taxon_num) == 1 or self.workflow:
self.auto_parFromfile()
else:
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Information)
msg.setText(
'Input files contain different numbers of sequences (which implies that some genes are missing), '
'execute Gblocks with most relaxed parameters to retain as much data as possible?'
)
msg.setWindowTitle("Gblocks")
list_detail = ["Seqs | Files"] + [
str(i).ljust(6) + "| " + str(dict_taxon_num[i])
for i in dict_taxon_num
]
msg.setDetailedText("\n".join(list_detail))
msg.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
if msg.exec_() == QMessageBox.Yes:
self.comboBox_10.setDisabled(True)
self.comboBox_2.setDisabled(True)
self.runAnyway = True
self.auto_parFromfile()
else:
return
# 输入序列
self.comboBox_4.refreshInputs(infiles)
def comboLink(self, text):
if text: # 有时候清空combobox会报错
list_first_opt = []
for i in range(int(text) + 1):
if i >= self.seq_num // 2 + 1:
list_first_opt.append(str(i))
self.combobox_refresh(self.comboBox_10, list_first_opt)
# self.comboBox_10.setCurrentIndex(0)
def run_code(self, commands):
startupINFO = None
if platform.system().lower() == "windows":
startupINFO = subprocess.STARTUPINFO()
startupINFO.dwFlags |= subprocess.STARTF_USESHOWWINDOW
startupINFO.wShowWindow = subprocess.SW_HIDE
self.gb_popen = subprocess.Popen(commands,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
startupinfo=startupINFO)
else:
self.gb_popen = subprocess.Popen(commands,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
startupinfo=startupINFO,
shell=True,
preexec_fn=os.setsid)
self.factory.emitCommands(self.logGuiSig, commands)
is_error = False ##判断是否出了error
while True:
QApplication.processEvents()
if self.isRunning():
try:
out_line = self.gb_popen.stdout.readline().decode(
"utf-8", errors='ignore')
except UnicodeDecodeError:
out_line = self.gb_popen.stdout.readline().decode(
"gbk", errors='ignore')
if out_line == "" and self.gb_popen.poll() is not None:
break
self.logGuiSig.emit(out_line.strip())
if "Execution terminated" in out_line:
is_error = True
else:
break
if is_error:
self.interrupt = True
self.gblocks_exception.emit(
"Error happened! Click <span style='font-weight:600; color:#ff0000;'>Show log</span> to see detail!"
)
self.gb_popen = None
def addText2Log(self, text):
if re.search(r"\w+", text):
self.textEdit_log.append(text)
with open(self.exportPath + os.sep + "PhyloSuite_Gblocks.log",
"a") as f:
f.write(text + "\n")
def gui4Log(self):
dialog = QDialog(self)
dialog.resize(800, 500)
dialog.setWindowTitle("Log")
gridLayout = QGridLayout(dialog)
horizontalLayout_2 = QHBoxLayout()
label = QLabel(dialog)
label.setText("Log of Gblocks:")
horizontalLayout_2.addWidget(label)
spacerItem = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
horizontalLayout_2.addItem(spacerItem)
toolButton = QToolButton(dialog)
icon2 = QIcon()
icon2.addPixmap(
QPixmap(
":/picture/resourses/interface-controls-text-wrap-512.png"))
toolButton.setIcon(icon2)
toolButton.setCheckable(True)
toolButton.setToolTip("Use Wraps")
toolButton.clicked.connect(self.setWordWrap)
toolButton.setChecked(True)
horizontalLayout_2.addWidget(toolButton)
pushButton = QPushButton("Save to file", dialog)
icon = QIcon()
icon.addPixmap(QPixmap(":/picture/resourses/Save-icon.png"))
pushButton.setIcon(icon)
pushButton_2 = QPushButton("Close", dialog)
icon = QIcon()
icon.addPixmap(QPixmap(":/picture/resourses/if_Delete_1493279.png"))
pushButton_2.setIcon(icon)
self.textEdit_log = QTextEdit(dialog)
self.textEdit_log.setReadOnly(True)
gridLayout.addLayout(horizontalLayout_2, 0, 0, 1, 2)
gridLayout.addWidget(self.textEdit_log, 1, 0, 1, 2)
gridLayout.addWidget(pushButton, 2, 0, 1, 1)
gridLayout.addWidget(pushButton_2, 2, 1, 1, 1)
pushButton.clicked.connect(self.save_log_to_file)
pushButton_2.clicked.connect(dialog.close)
dialog.setWindowFlags(dialog.windowFlags()
| Qt.WindowMinMaxButtonsHint)
return dialog
def setWordWrap(self):
button = self.sender()
if button.isChecked():
button.setChecked(True)
self.textEdit_log.setLineWrapMode(QTextEdit.WidgetWidth)
else:
button.setChecked(False)
self.textEdit_log.setLineWrapMode(QTextEdit.NoWrap)
def save_log_to_file(self):
content = self.textEdit_log.toPlainText()
fileName = QFileDialog.getSaveFileName(self, "Gblocks", "log",
"text Format(*.txt)")
if fileName[0]:
with open(fileName[0], "w", encoding="utf-8") as f:
f.write(content)
def collect_args(self):
self.files = self.comboBox_4.fetchListsText()
dict_abbre = {
"None": "n",
"With Half": "h",
"All": "a",
"Yes": "y",
"No": "n",
"Save": "y",
"Don't Save": "n",
"Save Text": "t",
"Save Short": "s"
}
if self.radioButton.isChecked():
self.t = "d"
elif self.radioButton_2.isChecked():
self.t = "p"
elif self.radioButton_3.isChecked():
self.t = "c"
self.b1 = self.comboBox_10.currentText()
self.b2 = self.comboBox_2.currentText()
self.b3 = str(self.spinBox_2.value())
self.b4 = str(self.spinBox_3.value())
self.b5 = dict_abbre[self.comboBox_5.currentText()]
self.b6 = " -b6=%s" % dict_abbre[
self.comboBox_13.currentText()] if self.t == "p" else ""
self.s = dict_abbre[self.comboBox_6.currentText()]
self.p = dict_abbre[self.comboBox_12.currentText()]
self.v = str(self.spinBox.value())
self.n = dict_abbre[self.comboBox_7.currentText()]
self.u = dict_abbre[self.comboBox_8.currentText()]
self.k = dict_abbre[self.comboBox_11.currentText()]
self.d = dict_abbre[self.comboBox_9.currentText()]
self.e = self.lineEdit_3.text()
prefix = "Ambiguously aligned fragments of %d alignments were removed in batches" % self.comboBox_4.count(
) if self.comboBox_4.count(
) > 1 else "Ambiguously aligned fragments of 1 alignment was removed"
self.description = '''%s using Gblocks (Talavera and Castresana, 2007) with the following parameter settings: minimum number of sequences for a conserved/flank position (%s/%s), maximum number of contiguous non-conserved positions (%s), minimum length of a block (%s), allowed gap positions (%s).''' % (
prefix, self.b1, self.b2, self.b3, self.b4,
self.comboBox_5.currentText().lower())
self.reference = "Talavera, G., Castresana, J., 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564-577."
def auto_parFromfile(self):
list_second_opt = [] # 设置第二个选项
self.seq_range_num = self.seq_num + 1 # 必须加1，参数才会正确
for j in range(self.seq_range_num):
if j >= self.seq_num // 2 + 1:
list_second_opt.append(str(j))
self.combobox_refresh(self.comboBox_2, list_second_opt)
# self.comboBox_2.setCurrentIndex(0)
list_first_opt = [] # 设置第一个选项
for k in range(int(self.comboBox_2.currentText()) + 1):
if k >= self.seq_num // 2 + 1:
list_first_opt.append(str(k))
self.combobox_refresh(self.comboBox_10, list_first_opt)
def check_MSA(self, files):
self.unaligns = []
self.dict_genes_alignments = OrderedDict()
parsefmt = Parsefmt("")
for num, eachFile in enumerate(files):
geneName = os.path.splitext(os.path.basename(eachFile))[0]
dict_taxon = parsefmt.readfile(eachFile)
if self.factory.is_aligned(dict_taxon):
self.dict_genes_alignments[geneName] = dict_taxon
else:
self.unaligned = True
self.unaligns.append(geneName)
# 补足数据
dict_warning_data = OrderedDict()
dict_maxTaxa = []
for k in self.dict_genes_alignments:
list_taxon = list(self.dict_genes_alignments[k].keys())
dict_maxTaxa.extend(list_taxon)
list_set_dict_maxTaxa = list(set(dict_maxTaxa))
self.seq_num = len(list_set_dict_maxTaxa)
self.auto_parFromfile()
for i in list_set_dict_maxTaxa:
lossingGene = []
for j in self.dict_genes_alignments:
if i not in self.dict_genes_alignments[j]:
keys = list(self.dict_genes_alignments[j].keys())
alignmentLenth = len(
self.dict_genes_alignments[j][keys[0]])
self.dict_genes_alignments[j][i] = "?" * alignmentLenth
lossingGene.append(j)
if lossingGene:
dict_warning_data[i] = lossingGene
# 覆盖以前的文件
self.input_files = []
convertfmt = Convertfmt(**{
"export_path": self.exportPath,
"export_fas": True
})
for name in self.dict_genes_alignments:
convertfmt.generate_each(self.dict_genes_alignments[name], name)
self.input_files.append(convertfmt.f6)
# 生成报错信息
if dict_warning_data:
max_len_taxa = len(max(list(dict_warning_data), key=len))
# 要大于species的占位符
max_len_taxa = max_len_taxa if max_len_taxa > 7 else 7
list_detail = [
"Species".ljust(max_len_taxa) + " |Missing genes"
] + [
str(i).ljust(max_len_taxa) + " |" + str(dict_warning_data[i])
for i in dict_warning_data
]
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Warning)
msg.setText(
"<p style='line-height:25px; height:25px'>Missing genes are replaced with '?' (see details or 'missing_genes.txt')</p>"
)
msg.setWindowTitle("Warning")
msg.setDetailedText("\n".join(list_detail))
msg.setStandardButtons(QMessageBox.Ok)
with open(self.exportPath + os.sep + "missing_genes.txt",
"w",
encoding="utf-8") as f:
f.write("\n".join(list_detail))
msg.exec_()
# if msg.exec_() == 1024: # QDialog.Accepted:
# if self.workflow:
# ##work flow跑的
# self.startButtonStatusSig.emit(
# [
# self.pushButton,
# self.progressBar,
# "workflow stop",
# self.exportPath,
# self.qss_file,
# self])
# self.workflow_finished.emit("finished")
# return
# self.startButtonStatusSig.emit(
# [self.pushButton, self.progressBar, "stop", self.exportPath, self.qss_file, self])
# self.focusSig.emit(self.exportPath)
def combobox_refresh(self, widget, list_items):
model = widget.model()
widget.clear()
for num, i in enumerate(list_items):
item = QStandardItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
widget.setCurrentIndex(0)
def isRunning(self):
'''判断程序是否运行,依赖进程是否存在来判断'''
return hasattr(self,
"gb_popen") and self.gb_popen and not self.interrupt
def popup_Gblocks_exception(self, text):
QMessageBox.information(
self, "Gblocks",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
if "Show log" in text:
self.on_pushButton_9_clicked()
def popupAutoDec(self, init=False):
self.init = init
self.factory.popUpAutoDetect("Gblocks", self.workPath,
self.auto_popSig, self)
def popupAutoDecSub(self, popupUI):
if not popupUI:
if not self.init:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>"
)
return
if not self.init: popupUI.checkBox.setVisible(False)
if popupUI.exec_() == QDialog.Accepted:
widget = popupUI.listWidget_framless.itemWidget(
popupUI.listWidget_framless.selectedItems()[0])
autoInputs = widget.autoInputs
self.input(autoInputs)
def fetchWorkflowSetting(self):
'''* Data type
* Minimum Number Of Sequences For A Conserved Position:
* Minimum Number Of Sequences For A Flank Position:
* Maximum Number Of Contiguous Nonconserved Positions:
* Minimum Length Of A Block:
* Allowed Gap Positions:'''
settings = '''<p class="title">***Gblocks***</p>'''
if self.radioButton.isChecked():
data_type = "Nucleotide"
elif self.radioButton_2.isChecked():
data_type = "Protein"
elif self.radioButton_3.isChecked():
data_type = "Codons"
settings += '<p>Data type: <a href="self.Gblocks_exe factory.highlightWidgets(x.radioButton,' \
'x.radioButton_2,x.radioButton_3)">%s</a></p>' % data_type
conserve_pos = self.comboBox_10.currentText()
if conserve_pos:
settings += '<p>Minimum Number Of Sequences For A Conserved Position: <a href="self.Gblocks_exe ' \
'comboBox_10.showPopup() factory.highlightWidgets(x.comboBox_10)">%s</a></p>' % conserve_pos
else:
settings += '<p>Minimum Number Of Sequences For A Conserved Position: <span style="font-weight:600; color:green;">auto detect when loading files</span></p>'
flank_pos = self.comboBox_2.currentText()
if flank_pos:
settings += '<p>Minimum Number Of Sequences For A Conserved Position: <a href="self.Gblocks_exe ' \
'comboBox_2.showPopup() factory.highlightWidgets(x.comboBox_2)">%s</a></p>' % flank_pos
else:
settings += '<p>Minimum Number Of Sequences For A Flank Position: <span style="font-weight:600; color:green;">auto detect when loading files</span></p>'
max_pos = self.spinBox_2.value()
settings += '<p>Maximum Number Of Contiguous Nonconserved Positions: ' \
'<a href="self.Gblocks_exe spinBox_2.setFocus() spinBox_2.selectAll()' \
' factory.highlightWidgets(x.spinBox_2)">%s</a></p>' % max_pos
min_block = self.spinBox_3.value()
settings += '<p>Minimum Length Of A Block: <a href="self.Gblocks_exe spinBox_3.setFocus() spinBox_3.selectAll()' \
' factory.highlightWidgets(x.spinBox_3)">%s</a></p>' % min_block
allow_gap = self.comboBox_5.currentText()
settings += '<p>Allowed Gap Positions: <a href="self.Gblocks_exe ' \
'comboBox_5.showPopup() factory.highlightWidgets(x.comboBox_5)">%s</a></p>' % allow_gap
return settings
def showEvent(self, event):
QTimer.singleShot(100, lambda: self.showSig.emit(self))
# self.showSig.emit(self)
def isFileIn(self):
return self.comboBox_4.count()
