class Lg_addFiles(QDialog, Ui_addFile, object):
closeGUI_signal = pyqtSignal()
inputSig = pyqtSignal(list, list, bool, str)
inputContentSig = pyqtSignal(str, str)
exception_signal = pyqtSignal(str)
progressDiologSig = pyqtSignal(int)
fastaDownloadFinishedSig = pyqtSignal(str)
inputFasSig = pyqtSignal(str, str)
def __init__(self, exportPath=None, parent=None):
super(Lg_addFiles, self).__init__(parent)
self.factory = Factory()
self.parent = parent
self.thisPath = self.factory.thisPath
self.exportPath = exportPath
# 保存设置
self.addFiles_settings = QSettings(
self.thisPath +
'/settings/addFiles_settings.ini',
QSettings.IniFormat)
self.closeGUI_signal.connect(self.close)
self.progressDiologSig.connect(self.runProgressDialog)
# self.close() 不能在信号槽里面
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
# 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)
self.setupUi(self)
self.guiRestore()
self.exception_signal.connect(self.popupException)
self.interrupt = False
self.label_3.clicked.connect(lambda : QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-1-1-Brief-example")))
def fetSeqFromNCBI(self, id_array):
batch_size = 20
count = len(id_array)
download_contents = ""
for start in range(0, count, batch_size):
if self.interrupt:
return
end = min(count, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > count:
batch_size = count - start
Entrez.email = self.email if self.email else "*****@*****.**"
fetch_handle = Entrez.efetch(db="nucleotide", rettype=self.rettype, retmode="text",
retstart=start, retmax=batch_size, id=id_array)
download_contents += fetch_handle.read()
self.progressDiologSig.emit(end * 100 / count)
if self.rettype == "gb":
self.inputContentSig.emit(
download_contents, self.outputPath)
else:
with open(self.outputPath + os.sep + self.fasta_file_name, "w", encoding="utf-8") as f:
f.write(download_contents)
self.fastaDownloadFinishedSig.emit(self.outputPath)
# result_handle = Entrez.efetch(
# db="nucleotide", rettype="gb", id=id_array, retmode="text")
# # with open(self.exportPath + os.sep + "new.gb", "w", encoding="utf-8") as f2:
# # f2.write(result_handle.read())
# self.inputContentSig.emit(
# result_handle.read(), [])
@pyqtSlot()
def on_pushButton_clicked(self):
self.outputPath = self.fetchOutputPath()
if self.parent.isWorkFolder(self.outputPath, mode="gb"):
files = QFileDialog.getOpenFileNames(
self, "Input GenBank Files", filter="GenBank and Fasta Format (*.gb *.gbk *.gbf *.gp *.gbff *.fas *.fasta);;")
if files[0]:
list_gbs = []
list_fas = []
for i in files[0]:
if os.path.splitext(i)[1].upper() in [".GB", ".GBK", ".GP", ".GBF", ".GBFF"]:
list_gbs.append(i)
elif os.path.splitext(i)[1].upper() in [".FAS", ".FASTA"]:
list_fas.append(i)
if list_gbs:
self.inputSig.emit(list_gbs, [], False, self.outputPath)
if list_fas:
fasContent = ""
for i in list_fas:
with open(i, encoding="utf-8", errors='ignore') as f:
fasContent += f.read() + "\n"
self.inputFasSig.emit(fasContent, self.outputPath)
self.close()
self.deleteLater()
del self
else:
files = QFileDialog.getOpenFileNames(
self, "Input Files",
filter="Supported Format (*.docx *.doc *.odt *.docm *.dotx *.dotm *.dot "
"*.fas *.fasta *.phy *.phylip *.nex *.nxs *.nexus);;")
if files[0]:
self.inputSig.emit([], files[0], False, self.outputPath)
self.close()
self.deleteLater()
del self
@pyqtSlot()
def on_pushButton_2_clicked(self):
# download
self.interrupt = False
text_content = self.plainTextEdit.toPlainText()
if text_content:
self.outputPath = self.fetchOutputPath()
self.rettype = "gb" if self.parent.isWorkFolder(self.outputPath, mode="gb") else "fasta"
if self.rettype == "fasta":
name, ok = QInputDialog.getText(
self, 'Set output file name', 'Output file name:', text="sequence.fas")
if ok:
self.fasta_file_name = name + ".fas" if "." not in name else name
if os.path.exists(self.outputPath + os.sep + self.fasta_file_name):
reply = QMessageBox.question(
self,
"Concatenate sequence",
"<p style='line-height:25px; height:25px'>The file exists, replace it?</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Cancel:
return
else:
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>Download canceled!</p>")
return
self.downloadState("start")
self.progressDialog = self.factory.myProgressDialog(
"Please Wait", "Downloading...", parent=self)
self.progressDialog.show()
self.id_array = re.split(r"\s|,", text_content)
while "" in self.id_array:
self.id_array.remove("")
self.email = self.lineEdit.text()
self.worker_download = WorkThread(self.run_command, parent=self)
self.progressDialog.canceled.connect(lambda: [setattr(self, "interrupt", True),
self.worker_download.stopWork(),
self.progressDialog.close(),
self.downloadState("stop")])
self.worker_download.start()
else:
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>Please input ID(s) first</p>")
@pyqtSlot()
def on_pushButton_8_clicked(self):
#search in NCBI
self.close()
self.parent.on_SerhNCBI_triggered()
@pyqtSlot()
def on_toolButton_clicked(self):
info = '''To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request.<br>
In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities.'''
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>%s</p>"%info)
def run_command(self):
try:
self.fetSeqFromNCBI(self.id_array)
self.closeGUI_signal.emit()
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)
# self.popupException(self.exceptionInfo) # 激发这个信号
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_()
self.pushButton_2.setEnabled(True)
self.pushButton_2.setStyleSheet(self.qss_file)
self.pushButton_2.setText("Start")
def guiSave(self):
# Save geometry
self.addFiles_settings.setValue('size', self.size())
# self.addFiles_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, QTextBrowser):
# # save combobox selection to registry
# htmlText = obj.toHtml()
# self.addFiles_settings.setValue(name, htmlText)
def guiRestore(self):
# Restore geometry
self.resize(self.addFiles_settings.value('size', QSize(500, 500)))
# self.move(self.addFiles_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox":
allItems = self.factory.fetchAllWorkFolders(self.exportPath)
model = obj.model()
obj.clear()
for num, i in enumerate(allItems):
if self.parent.isWorkFolder(i, mode="gb"):
text = "\"%s\" in GenBank_File (GenBank format)"%os.path.basename(i)
else:
text = "\"%s\" in Other_File" % os.path.basename(i)
item = QStandardItem(text)
item.setToolTip(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 self.parent.isWorkFolder(self.exportPath, mode="gb"):
obj.setCurrentText("\"%s\" in GenBank_File (GenBank format)"%os.path.basename(self.exportPath))
else:
obj.setCurrentText("\"%s\" in Other_File" % os.path.basename(self.exportPath))
def closeEvent(self, event):
self.interrupt = True
if hasattr(self, "worker_download"):
self.worker_download.stopWork()
if hasattr(self, "progressDialog"):
self.progressDialog.close()
self.guiSave()
def runProgressDialog(self, num):
oldValue = self.progressDialog.value()
done_int = int(num)
if done_int > oldValue:
self.progressDialog.setProperty("value", done_int)
QCoreApplication.processEvents()
if done_int == 100:
self.progressDialog.close()
def fetchOutputPath(self):
index = self.comboBox.currentIndex()
return self.comboBox.itemData(index, role=Qt.ToolTipRole)
def downloadState(self, state):
if state == "start":
self.pushButton_2.setEnabled(False) # 使之失效
self.pushButton_2.setStyleSheet(
'QPushButton {color: red; background-color: rgb(219, 217, 217)}')
self.pushButton_2.setText("Downloading...")
elif state == "stop":
self.pushButton_2.setText("Download")
self.pushButton_2.setStyleSheet(self.qss_file)
self.pushButton_2.setEnabled(True)
class ConvertFMT(QDialog, Ui_ConverFMT, 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)
unalignedSig = pyqtSignal(list)
def __init__(self,
workPath=None,
focusSig=None,
autoFiles=None,
parent=None):
super(ConvertFMT, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoFiles = autoFiles
self.setupUi(self)
# 保存设置
self.convertFmt_settings = QSettings(
self.thisPath + '/settings/convertFmt_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.convertFmt_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.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) #自动识别可用的输入
self.unalignedSig.connect(self.popupUnaligns)
# 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_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-8-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
AllItems = self.comboBox_4.fetchListsText()
if AllItems:
self.dict_args = {}
self.dict_args["exception_signal"] = self.exception_signal
self.dict_args["unaligned_signal"] = self.unalignedSig
self.dict_args["progressSig"] = self.progressSig
self.dict_args["files"] = AllItems
self.dict_args["workPath"] = self.workPath
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.dict_args["export_path"] = self.factory.creat_dirs(
self.workPath + os.sep + "convertFmt_results" + os.sep +
self.output_dir_name)
self.dict_args["export_phylip"] = self.checkBox.isChecked()
self.dict_args["export_nex"] = self.checkBox_2.isChecked()
self.dict_args["export_nexi"] = self.checkBox_3.isChecked()
self.dict_args["export_axt"] = self.checkBox_13.isChecked()
self.dict_args["export_paml"] = self.checkBox_5.isChecked()
self.dict_args["export_fas"] = self.checkBox_12.isChecked()
self.dict_args["export_stat"] = self.checkBox_9.isChecked()
if True not in list(self.dict_args.values()):
QMessageBox.critical(
self, "Convert Sequence Format",
"<p style='line-height:25px; height:25px'>Please select output format(s) first!</p>"
)
self.checkBox.setChecked(True)
return
ok = self.factory.remove_dir(self.dict_args["export_path"],
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
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.critical(
self, "Convert Sequence Format",
"<p style='line-height:25px; height:25px'>Please input files first!</p>"
)
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
open files
"""
files = QFileDialog.getOpenFileNames(
self,
"Input Files",
filter=
"Supported Format(*.fas *.fasta *.phy *.phylip *.nex *.nxs *.nexus);;"
)
if files[0]:
self.input(files[0])
def run_command(self):
try:
# 先清空文件夹
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start",
self.dict_args["export_path"], self.qss_file, self
])
convertFmt = Convertfmt(**self.dict_args)
convertFmt.exec_()
if convertFmt.error_message:
self.exception_signal.emit(convertFmt.error_message) # 激发这个信号
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.dict_args["export_path"], self.qss_file, self
])
elif convertFmt.unaligns:
self.unalignedSig.emit(convertFmt.unaligns)
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.dict_args["export_path"], self.qss_file, self
])
else:
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "stop",
self.dict_args["export_path"], self.qss_file, self
])
self.focusSig.emit(self.dict_args["export_path"])
time_end = datetime.datetime.now()
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (
str(time_start), str(time_end), str(time_end - time_start))
with open(self.dict_args["export_path"] + os.sep + "summary.txt",
"w",
encoding="utf-8") as f:
f.write(
"If you use PhyloSuite, please cite:\nZhang, D., Gao, F., Li, W.X., Jakovlić, I., Zou, H., Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. bioRxiv, doi: 10.1101/489088.\n\n"
+ self.time_used_des)
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.dict_args["export_path"], self.qss_file, self
])
def guiSave(self):
# Save geometry
self.convertFmt_settings.setValue('size', self.size())
# self.convertFmt_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, QCheckBox):
state = obj.isChecked()
self.convertFmt_settings.setValue(name, state)
if isinstance(obj, QRadioButton):
state = obj.isChecked()
self.convertFmt_settings.setValue(name, state)
def guiRestore(self):
# Restore geometry
self.resize(self.convertFmt_settings.value('size', QSize(500, 500)))
# self.move(self.convertFmt_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if self.autoFiles:
self.input(self.autoFiles)
else:
self.input([])
if isinstance(obj, QCheckBox):
value = self.convertFmt_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QRadioButton):
value = self.convertFmt_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
def input(self, list_inputs):
self.comboBox_4.refreshInputs(list_inputs)
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()
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()]
files = [
i for i in files if os.path.splitext(i)[1].upper() in [
".FAS", ".FASTA", ".PHY", ".PHYLIP", ".NEX", ".NXS",
".NEXUS"
]
]
self.input(files)
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(ConvertFMT, self).eventFilter(obj, event) # 0
def popupUnaligns(self, message):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Warning)
msg.setText(
"<p style='line-height:25px; height:25px'>Unaligned sequences found, see details</p>"
)
msg.setWindowTitle("Warning")
msg.setDetailedText("Unaligned sequences: " + ",".join(message))
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def popupAutoDec(self):
popupUI = self.factory.popUpAutoDetect("format conversion",
self.workPath, self)
if not popupUI:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>"
)
return
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)
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 ExtractGB(QDialog, Ui_Extractor, 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
threadFinished = pyqtSignal()
startButtonStatusSig = pyqtSignal(list)
def __init__(
self,
gb_files=None,
list_names=None,
workPath=None,
totleID=None,
clearFolderSig=None,
focusSig=None,
parent=None):
super(ExtractGB, self).__init__(parent)
self.parent = parent
self.setupUi(self)
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.gb_files = gb_files
self.workPath = workPath
self.totleID = totleID
self.clearFolderSig = clearFolderSig
self.list_names = list_names
self.focusSig = focusSig
self.installEventFilter(self)
self.dict_icon = {
"rectangle": ":/itol_domain/resourses/itol/re.png",
"horizontal hexagon": ":/itol_domain/resourses/itol/hh.png",
"vertical hexagon": ":/itol_domain/resourses/itol/hv.png",
"ellipse": ":/itol_domain/resourses/itol/el.png",
"rhombus (diamond)": ":/itol_domain/resourses/itol/di.png",
"right pointing triangle": ":/itol_domain/resourses/itol/tr.png",
"left pointing triangle": ":/itol_domain/resourses/itol/tl.png",
"left pointing pentagram": ":/itol_domain/resourses/itol/pl.png",
"right pointing pentagram": ":/itol_domain/resourses/itol/pr.png",
"up pointing pentagram": ":/itol_domain/resourses/itol/pu.png",
"down pointing pentagram": ":/itol_domain/resourses/itol/pd.png",
"octagon": ":/itol_domain/resourses/itol/oc.png",
"rectangle (gap)": ":/itol_domain/resourses/itol/gp.png"}
self.dict_shape = {
"rectangle": "RE",
"horizontal hexagon": "HH",
"vertical hexagon": "HV",
"ellipse": "EL",
"rhombus (diamond)": "DI",
"right pointing triangle": "TR",
"left pointing triangle": "TL",
"left pointing pentagram": "PL",
"right pointing pentagram": "PR",
"up pointing pentagram": "PU",
"down pointing pentagram": "PD",
"octagon": "OC",
"rectangle (gap)": "GP"}
self.showOn()
self.extractGB_settings = QSettings(
self.thisPath + '/settings/extractGB_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.extractGB_settings.setFallbacksEnabled(False)
self.settings_ini = QSettings(self.thisPath + '/settings/setting_settings.ini', QSettings.IniFormat)
self.settings_ini.setFallbacksEnabled(False)
# 保存主界面设置
self.mainwindow_settings = QSettings(
self.thisPath + '/settings/mainwindow_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.mainwindow_settings.setFallbacksEnabled(False)
# 恢复用户的设置
self.guiRestore()
# 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)
self.progressSig.connect(self.runProgress)
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.tableWidget_2.installEventFilter(self)
self.table_popMenu = QMenu(self)
self.Copy = QAction("Copy", self,
statusTip="Copy color(s)",
shortcut="Ctrl+C",
triggered=self.copyColor)
self.Cut = QAction("Cut", self,
statusTip="Cut color(s)",
shortcut="Ctrl+X",
triggered=self.cutColor)
self.Paste = QAction("Paste", self,
statusTip="Paste color(s)",
shortcut="Ctrl+V",
triggered=self.pasteColor)
self.remove = QAction("Delete", self,
shortcut=QKeySequence.Delete,
statusTip="Remove color(s)",
triggered=self.on_pushButton_9_clicked)
self.table_popMenu.addAction(self.Copy)
self.table_popMenu.addAction(self.Cut)
self.table_popMenu.addAction(self.Paste)
self.table_popMenu.addAction(self.remove)
self.tableWidget_2.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableWidget_2.customContextMenuRequested.connect(lambda x: self.table_popMenu.exec_(QCursor.pos()))
self.comboBox_6.activated[str].connect(self.switchSeqType)
# self.checkBox.toggled.connect(self.judgeCodonW)
self.switchSeqType(self.comboBox_6.currentText())
# 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_2.toolButton.setMenu(menu)
self.pushButton_2.toolButton.menu().installEventFilter(self)
self.factory.swithWorkPath(self.work_action, init=True, parent=self) # 初始化一下
## brief demo
self.label_3.clicked.connect(lambda: QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-1-1-Brief-example")))
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
execute program
"""
self.dict_args = {}
self.dict_args["progressSig"] = self.progressSig
self.dict_args["gb_files"] = self.gb_files
self.dict_args["workPath"] = self.workPath
# 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 + "extract_results" + os.sep + self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
self.dict_args["codon"] = str(
self.comboBox_9.currentText()).split(" ")[0]
self.dict_args["Name Type"] = [self.comboBox_4.itemText(i) for i in range(self.comboBox_4.count())
if self.comboBox_4.model().item(i).checkState() == Qt.Checked]
# self.dict_args["Gene Number"] = str(
# self.comboBox_8.currentText())
# bool
self.dict_args["if ignore duplicated"] = True #self.checkBox_2.isChecked()
self.dict_args["if statistics"] = True #self.checkBox_3.isChecked()
self.dict_args["if itol"] = self.groupBox_4.isChecked()
self.dict_args["totleID"] = self.totleID
self.dict_args["seq type"] = str(self.comboBox_6.currentText())
for row, row_text in enumerate(
["atp", "nad", "cytb", "cox", "rRNA", "tRNA", "NCR"]):
for column, column_text in enumerate(
["checked", "colour", "length", "shape"]):
if column == 0:
self.dict_args[row_text + column_text] = True if self.tableWidget.item(
row, column).checkState() == Qt.Checked else False # bool
elif column == 1:
self.dict_args[row_text +
column_text] = self.tableWidget.item(row, column).text()
elif column == 2:
self.dict_args[row_text +
column_text] = self.tableWidget.item(row, column).text()
elif column == 3:
shape_combo = self.tableWidget.cellWidget(row, column)
shape = shape_combo.currentText()
self.dict_args[row_text +
column_text] = self.dict_shape[shape] # 转为缩写形式
self.dict_args["gene interval"] = self.doubleSpinBox.value()
self.dict_args["included_lineages"] = [self.comboBox_7.itemText(i) for i in range(self.comboBox_7.count())
if self.comboBox_7.model().item(i).checkState() == Qt.Checked]
# {"Family":["red", "green", ""]}
dict_color_array = self.getLineageColor()
for i in dict_color_array:
while "" in dict_color_array[i]:
# 删除空行
dict_color_array[i].remove("")
self.dict_args["lineage color"] = dict_color_array
##提取的设置
dict_extract_settings = copy.deepcopy(self.dict_gbExtract_set[self.comboBox_6.currentText()])
#提取所有的话，记得先判断有没有那个键
extract_all_features = dict_extract_settings.pop("extract all features") if "extract all features" \
in dict_extract_settings else False
self.dict_args["extract_intergenic_regions"] = dict_extract_settings.pop("extract intergenic regions") if "extract intergenic regions" \
in dict_extract_settings else True
self.dict_args["extract_overlapping_regions"] = dict_extract_settings.pop("extract overlapping regions") if "extract overlapping regions" \
in dict_extract_settings else True
self.dict_args["intergenic_regions_threshold"] = dict_extract_settings.pop("intergenic regions threshold") if "intergenic regions threshold" \
in dict_extract_settings else 200
self.dict_args["overlapping_regions_threshold"] = dict_extract_settings.pop(
"overlapping regions threshold") if "overlapping regions threshold" \
in dict_extract_settings else 1
self.dict_args["features"] = dict_extract_settings.pop("Features to be extracted") if not extract_all_features else "All"
# self.dict_args["features"] = "All" if self.extract_all_features else self.dict_args["features"]
name_unify = dict_extract_settings.pop("Names unification")
self.dict_args["replace"] = {i[0]: i[1] for i in name_unify}
self.dict_args["extract_list_gene"] = dict_extract_settings.pop("extract listed gene") if "extract listed gene" \
in dict_extract_settings else False
self.dict_args["qualifiers"] = dict_extract_settings ###只剩下qualifier的设置
self.dict_args["extract_entire_seq"] = self.radioButton.isChecked()
self.dict_args["entire_seq_name"] = self.lineEdit.text() if self.lineEdit.text() else "sequence"
ok = self.factory.remove_dir(self.dict_args["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
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
def run_command(self):
try:
# 清空文件夹再生成结果,放在这里执行好统一管理报错
# self.clearFolderSig.emit(self.dict_args["exportPath"])
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit(
[self.pushButton_2, self.progressBar, "start", self.dict_args["exportPath"], self.qss_file, self])
if (self.dict_args["seq type"] == "Mitogenome") and (not self.dict_args["extract_entire_seq"]):
# 如果是整个序列提取，也不能用这个
extract = GBextract_MT(**self.dict_args)
extract._exec()
else:
extract = GBextract(**self.dict_args)
extract._exec()
# extract = GBextract(**self.dict_args)
if extract.Error_ID:
stopStatus = extract.Error_ID
elif extract.source_feature_IDs:
stopStatus = "extract_no_feature%s"%", ".join(extract.source_feature_IDs)
else:
stopStatus = "stop"
self.startButtonStatusSig.emit(
[self.pushButton_2, self.progressBar, stopStatus, self.dict_args["exportPath"], self.qss_file, self])
self.focusSig.emit(self.dict_args["exportPath"])
time_end = datetime.datetime.now()
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (str(time_start), str(time_end),
str(time_end - time_start))
with open(self.dict_args["exportPath"] + os.sep + "summary.txt", "w", encoding="utf-8") as f:
f.write("If you use PhyloSuite, please cite:\nZhang, D., Gao, F., Li, W.X., Jakovlić, I., Zou, H., "
"Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop "
"platform for streamlined molecular sequence data management and evolutionary phylogenetics "
"studies. bioRxiv, doi: 10.1101/489088.\n\n" + self.time_used_des
+ "For the summary of this extraction, please see \"overview.csv\"")
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_2, self.progressBar, "except", self.dict_args["exportPath"], self.qss_file, self])
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
self.close()
@pyqtSlot()
def on_pushButton_6_clicked(self):
"""
Add row
"""
currentRows = self.tableWidget_2.rowCount()
self.tableWidget_2.setRowCount(currentRows + 1)
for column in range(self.tableWidget_2.columnCount()):
item = QTableWidgetItem("")
item.setToolTip("Double click to set colors")
self.tableWidget_2.setItem(currentRows, column, item)
@pyqtSlot()
def on_pushButton_8_clicked(self):
"""
delete row
"""
selecteditems = self.tableWidget_2.selectedItems()
rows = sorted(set([i.row() for i in selecteditems]), reverse=True)
for row in rows:
self.tableWidget_2.removeRow(row)
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
delete cell
"""
selecteditems = self.tableWidget_2.selectedItems()
if selecteditems:
for i in selecteditems:
i.setText("")
i.setBackground(QColor('transparent'))
@pyqtSlot()
def on_toolButton_3_clicked(self):
"""
GenBank file extract settings
"""
self.extract_setting = ExtractSettings(self)
self.extract_setting.closeSig.connect(self.displaySettings)
# 添加最大化按钮
self.extract_setting.setWindowFlags(self.extract_setting.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.extract_setting.exec_()
@pyqtSlot()
def on_pushButton_10_clicked(self):
"""
GenBank file lineage recognization settings
"""
self.setting = Setting(self)
self.setting.display_table(self.setting.listWidget.item(0))
self.setting.closeSig.connect(self.updateLineageCombo)
self.setting.closeSig.connect(self.updateLineageTable)
self.setting.setWindowFlags(self.setting.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.setting.exec_()
def showOn(self):
list_color = [
"#ffff33",
"#99ffff",
"#ff9999",
"#6699ff",
"#DAA520",
"#ccff00",
"#bfbfbf"]
self.tableWidget.itemClicked.connect(self.handleItemClicked)
for row in range(self.tableWidget.rowCount()):
# 2列颜色 (必须初始化一个item，不然恢复界面设置会出错)
item2 = QTableWidgetItem(list_color[row])
item2.setBackground(QColor(list_color[row]))
self.tableWidget.setItem(row, 1, item2)
model = QStandardItemModel()
for i in self.dict_icon:
item = QStandardItem(i)
item.setIcon(QIcon(self.dict_icon[i]))
font = item.font()
font.setPointSize(13)
item.setFont(font)
model.appendRow(item)
comb_box = MyComboBox(self)
comb_box.setModel(model)
# 改变icon大小
view = comb_box.view()
view.setIconSize(QSize(38, 38))
self.tableWidget.setCellWidget(row, 3, comb_box)
self.tableWidget.resizeColumnsToContents()
self.tableWidget.verticalHeader().setVisible(False)
def handleItemClicked(self, item):
if item.column() == 1:
color = QColorDialog.getColor(QColor(item.text()), self)
if color.isValid():
item.setText(color.name())
item.setBackground(color)
self.tableWidget.clearSelection()
def handleItemClicked_2(self, item):
color = QColorDialog.getColor(QColor(item.text()), self)
if color.isValid():
item.setText(color.name())
item.setBackground(color)
self.tableWidget_2.clearSelection()
def guiSave(self):
# Save geometry
self.extractGB_settings.setValue('size', self.size())
# self.extractGB_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 in ["comboBox_7", "comboBox_4"]:
dict_state = {}
for i in range(obj.count()):
text = obj.itemText(i)
state = 2 if obj.model().item(i).checkState() == Qt.Checked else 0
dict_state[text] = state
self.extractGB_settings.setValue(name, dict_state)
elif name != "comboBox_5":
text = obj.currentText()
if text:
allItems = [
obj.itemText(i) for i in range(obj.count())]
allItems.remove(text)
sortItems = [text] + allItems
self.extractGB_settings.setValue(name, sortItems)
if isinstance(obj, QGroupBox):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QRadioButton):
state = obj.isChecked()
self.extractGB_settings.setValue(name, state)
if isinstance(obj, QTableWidget):
if name == "tableWidget":
array = [] # 每一行存：checked, color, length, index_text
for row in range(obj.rowCount()):
checked = "true" if obj.item(
row, 0).checkState() == Qt.Checked else "false"
colour = obj.item(row, 1).text()
length = obj.item(row, 2).text()
shape_combo = obj.cellWidget(row, 3)
shape = shape_combo.currentText()
array.append([checked, colour, length, shape])
self.extractGB_settings.setValue(name, array)
elif name == "tableWidget_2":
dict_color_array = self.getLineageColor()
self.extractGB_settings.setValue(name, dict_color_array)
if isinstance(obj, QTabWidget):
index = obj.currentIndex()
self.extractGB_settings.setValue(name, index)
if isinstance(obj, QDoubleSpinBox):
value = obj.value()
self.extractGB_settings.setValue(name, value)
if isinstance(obj, QLineEdit):
text = obj.text()
self.extractGB_settings.setValue(name, text)
def guiRestore(self):
# Restore geometry
self.resize(self.extractGB_settings.value('size', QSize(571, 680)))
if self.height() < 640:
self.resize(QSize(571, 650))
# self.move(self.extractGB_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox_5":
# 展示输入
model = obj.model()
obj.clear()
for num, i in enumerate(self.list_names):
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)
self.changeLable()
elif name == "comboBox_6":
self.displaySettings()
elif name == "comboBox_7":
self.updateLineageCombo()
elif name == "comboBox_4":
key = re.sub(r"/|\\", "_", self.workPath) + "_availableInfo"
value = self.mainwindow_settings.value(
key, None)
if value:
source_keys = value[3][1]
else:
source_keys = None
items = ["Organism", "ID", "Name", "Length", "Description", "Date"] + source_keys \
if source_keys else ["Organism", "ID", "Name", "Length"]
ini_state = {}.fromkeys(items, 0) # 2代表选中
ini_state["Organism"] = 2
ini_state["Name"] = 2
dict_name_state = self.extractGB_settings.value("comboBox_4", ini_state)
if type(dict_name_state) != dict:
dict_name_state = ini_state
self.comboBox_4.sep = "_"
model = self.comboBox_4.model()
self.comboBox_4.clear()
for num, text in enumerate(items):
item = QStandardItem(str(text))
state = dict_name_state[text] if text in dict_name_state else ini_state[text] # 测试一下
item.setCheckState(int(state))
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.comboBox_4.setTopText()
self.comboBox_4.view().pressed.connect(self.judgeName)
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
values = self.extractGB_settings.value(name, allItems)
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, QGroupBox):
# 如果没有name，就设置为True
state = self.extractGB_settings.value(name, "true")
obj.setChecked(self.factory.str2bool(state))
if isinstance(obj, QCheckBox):
value = self.extractGB_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QRadioButton):
value = self.extractGB_settings.value(
name, "first") # get stored value from registry
if value != "first":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QTableWidget):
if name == "tableWidget":
# 每一行存：checked, color, length, index_text
ini_array = [
[
'true', '#ffff33', '25', 'rectangle'], [
'true', '#99ffff', '25', 'rectangle'], [
'true', '#ff9999', '30', 'rectangle'], [
'true', '#6699ff', '25', 'rectangle'], [
'true', '#DAA520', '18', 'rectangle'], [
'true', '#ccff00', '15', 'rectangle'], [
'false', '#bfbfbf', '15', 'ellipse']]
array = self.extractGB_settings.value(name, ini_array)
for row in range(obj.rowCount()):
ifChecked = Qt.Checked if array[row][
0] == "true" else Qt.Unchecked
obj.item(row, 0).setCheckState(ifChecked)
obj.item(row, 1).setText(array[row][1])
obj.item(row, 1).setBackground(QColor(array[row][1]))
obj.item(row, 2).setText(array[row][2])
shape = array[row][3]
shape_combo = obj.cellWidget(row, 3)
shape_combo_index = shape_combo.findText(shape)
if shape_combo_index == -1: # add to list if not found
shape_combo.insertItems(0, [value])
index = shape_combo.findText(value)
shape_combo.setCurrentIndex(index)
else:
# preselect a combobox value by index
shape_combo.setCurrentIndex(shape_combo_index)
elif name == "tableWidget_2":
self.updateLineageTable()
if isinstance(obj, QTabWidget):
index = self.extractGB_settings.value(name, 0)
obj.setCurrentIndex(int(index))
if isinstance(obj, QDoubleSpinBox):
value = self.extractGB_settings.value(name, 1.0)
obj.setValue(float(value))
if isinstance(obj, QLineEdit):
text = self.extractGB_settings.value(name, "first")
if text != "first":
obj.setText(text)
def popupException(self, 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)
elif "Permission" in exception:
reply = QMessageBox.critical(
self,
"Extract sequence",
"<p style='line-height:25px; height:25px'>Error happened, please close the window and try again!</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Yes:
self.close()
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 closeEvent(self, event):
self.guiSave()
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 eventFilter(self, obj, event):
name = obj.objectName()
if isinstance(obj, QTableWidget):
if event.type() == QEvent.KeyPress: # 首先得判断type
modifiers = QApplication.keyboardModifiers()
if name == "tableWidget_2":
if event.key() == Qt.Key_Delete:
self.on_pushButton_9_clicked()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_C):
self.copyColor()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_X):
self.cutColor()
return True
if (modifiers == Qt.ControlModifier) and (
event.key() == Qt.Key_V):
self.pasteColor()
return True
if (event.type() == QEvent.Show) and (obj == self.pushButton_2.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_2.toolButton.menu().pos().x()
menu_width = self.pushButton_2.toolButton.menu().size().width()
button_width = self.pushButton_2.toolButton.size().width()
pos = QPoint(menu_x_pos - menu_width + button_width,
self.pushButton_2.toolButton.menu().pos().y())
self.pushButton_2.toolButton.menu().move(pos)
return True
return super(ExtractGB, self).eventFilter(obj, event)
def changeLable(self):
count = str(self.comboBox_5.count())
self.label_4.setText("Inputs (" + count + "):")
def getLineageColor(self):
dict_color_array = OrderedDict()
columnNum = self.tableWidget_2.columnCount()
rowNum = self.tableWidget_2.rowCount()
for column in range(columnNum):
headerText = self.tableWidget_2.horizontalHeaderItem(column).text()
list_columnText = []
for row in range(rowNum):
if self.tableWidget_2.item(row, column):
list_columnText.append(
self.tableWidget_2.item(row, column).text())
dict_color_array[headerText] = list_columnText
return dict_color_array
def copyColor(self):
selecteditems = self.tableWidget_2.selectedItems()
if selecteditems:
list_selItem_text = [i.text() for i in selecteditems]
QApplication.clipboard().setText("\t".join(list_selItem_text))
def cutColor(self):
selecteditems = self.tableWidget_2.selectedItems()
list_selItem_text = []
if selecteditems:
for i in selecteditems:
list_selItem_text.append(i.text())
i.setText("")
i.setBackground(QColor('transparent'))
QApplication.clipboard().setText("\t".join(list_selItem_text))
def pasteColor(self):
colors = QApplication.clipboard().text()
list_colors = re.split(r"\s+|,", colors)
while "" in list_colors:
list_colors.remove("")
selecteditems = self.tableWidget_2.selectedItems()
for num, i in enumerate(selecteditems):
if (num+1) <= len(list_colors):
color = list_colors[num]
qcolor = QColor(color)
if not qcolor.isValid():
continue
i.setText(color)
i.setBackground(qcolor)
def displaySettings(self):
###提取的设置
self.GenBankExtract_settings = QSettings(
self.thisPath + '/settings/GenBankExtract_settings.ini', QSettings.IniFormat)
# File only, no fallback to registry or or.
self.GenBankExtract_settings.setFallbacksEnabled(False)
self.dict_gbExtract_set = self.GenBankExtract_settings.value("set_version")
# self.extract_list_gene = self.factory.str2bool(self.GenBankExtract_settings.value("extract listed gene",
# "false"))
# self.extract_all_features = self.factory.str2bool(self.GenBankExtract_settings.value("extract all features",
#
# "false"))
if self.dict_gbExtract_set:
self.allVersions = list(self.dict_gbExtract_set.keys())
model = self.comboBox_6.model()
self.comboBox_6.clear()
for num, i in enumerate(self.allVersions + [">>>More<<<"]):
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)
self.switchSeqType(self.comboBox_6.currentText())
def switchSeqType(self, text):
###保存version顺序
if text == ">>>More<<<":
QDesktopServices.openUrl(QUrl("https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/customize_extraction/"))
self.comboBox_6.setCurrentIndex(0)
return
if text != self.allVersions[0]:
if text in self.allVersions:
list_now_versions = copy.deepcopy(self.allVersions)
list_now_versions.remove(text)
reorder_list = [text] + list_now_versions
self.dict_gbExtract_set = OrderedDict((i, self.dict_gbExtract_set[i]) for i in reorder_list)
self.GenBankExtract_settings.setValue('set_version', self.dict_gbExtract_set)
###控制itol
if text != "Mitogenome":
targetIndex = "null"
for index in range(self.tabWidget.count()):
if self.tabWidget.tabText(index) == "Gene order display":
targetIndex = index
if targetIndex != "null":
self.hiddenIndex = targetIndex
self.hiddenWidget = self.tabWidget.widget(self.hiddenIndex)
self.hiddenTabText = self.tabWidget.tabText(self.hiddenIndex)
self.tabWidget.removeTab(self.hiddenIndex)
self.hiddenFlag = True
else:
if hasattr(self, "hiddenFlag") and self.hiddenFlag:
self.tabWidget.insertTab(self.hiddenIndex, self.hiddenWidget, self.hiddenTabText)
self.hiddenFlag = False
self.tabWidget.setCurrentIndex(0)
def updateLineageTable(self):
# tableWidget_2
self.tableWidget_2.itemDoubleClicked.connect(self.handleItemClicked_2)
ini_data = [['Class', 'Order', 'Superfamily', 'Family', 'Subfamily', 'Genus'],
[['', '*tera', '*dea', '*dae', '*nae', ''],
['', '', '*ida', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', '']]]
header, array = self.settings_ini.value("Taxonomy Recognition", ini_data)
countColumn = len(header)
self.tableWidget_2.setColumnCount(countColumn)
ini_dict_array = OrderedDict()
for i in header:
ini_dict_array[i] = [""] * 6
familyColor = [
"#81C7D6", "#FF0033", "#6A00D1", "#49BF4E", "#AA538B", "#FF99CC"]
ini_dict_array[
"Family"] = familyColor if "Family" in ini_dict_array else ini_dict_array["Family"]
self.tableWidget_2.setHorizontalHeaderLabels(
header)
dict_array = self.extractGB_settings.value(
"tableWidget_2", ini_dict_array)
maxRow = len(max(list(dict_array.values()), key=len))
self.tableWidget_2.setRowCount(maxRow)
if len(ini_dict_array) > len(dict_array):
# 如果用户添加了lineage
list_differ = list(
set(ini_dict_array.keys()).difference(set(dict_array.keys())))
for i in list_differ:
# 加上这个lineage
dict_array[i] = [""] * maxRow
for column, columnText in enumerate(header):
for row, rowText in enumerate(dict_array[columnText]):
item = QTableWidgetItem(rowText)
item.setToolTip("Double click to set colors")
color = QColor(rowText)
if color.isValid():
item.setBackground(color)
self.tableWidget_2.setItem(row, column, item)
def updateLineageCombo(self):
ini_data = [['Class', 'Order', 'Superfamily', 'Family', 'Subfamily', 'Genus'],
[['', '*tera', '*dea', '*dae', '*nae', ''],
['', '', '*ida', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', ''],
['', '', '', '', '', '']]]
header, array = self.settings_ini.value("Taxonomy Recognition", ini_data)
ini_state = {}.fromkeys(header, 2) # 2代表选中
dict_lng_state = self.extractGB_settings.value("comboBox_7", ini_state)
model = self.comboBox_7.model()
self.comboBox_7.clear()
for num, text in enumerate(header):
item = QStandardItem(text)
state = dict_lng_state[text] if text in dict_lng_state else ini_state[text] # 测试一下
item.setCheckState(int(state))
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
self.comboBox_7.setTopText()
def judgeName(self):
if not set(["Organism", "ID", "Name"]).intersection(set(self.comboBox_4.topText.split("_"))):
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>At least one of the following should be retained: \"Organism\", \"ID\", \"Name\"</p>")
self.comboBox_4.item.setCheckState(Qt.Checked)
self.comboBox_4.setTopText()
def judgeCodonW(self, bool_):
if bool_:
pass
class SerhNCBI(QMainWindow, Ui_SerhNCBI, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
updateSig = pyqtSignal(list)
searchSig = pyqtSignal(str)
progressBarSig = pyqtSignal(int) # 控制进度条
progressDiologSig = pyqtSignal(int)
ctrlItemsSig = pyqtSignal(int)
inputContentSig = pyqtSignal(str, str)
downloadFinished = pyqtSignal()
fastaDownloadFinishedSig = pyqtSignal(str)
def __init__(self, workPath=None, parent=None):
super(SerhNCBI, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.setupUi(self)
# 保存设置
self.serhNCBI_settings = QSettings(
self.thisPath + '/settings/serhNCBI_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.serhNCBI_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.progressSig.connect(self.runProgress)
# self.logGuiSig.connect(self.addText2Log)
self.lineEdit.buttonSearch.clicked.connect(lambda: [
self.startSearch(),
self.sync_completer_texts(self.lineEdit.text())
])
self.lineEdit.buttonStop.clicked.connect(self.stopSearch)
# self.lineEdit.completer().popup().show()
# self.lineEdit.clicked.connect(lambda : self.lineEdit.completer().popup())
self.dict_ncbi_headers = {
"GBSeq_accession-version": "ID",
"GBSeq_definition": "Description",
"GBSeq_organism": "Organism",
"GBSeq_length": "Length",
"GBSeq_update-date": "Update date",
"GBSeq_taxonomy": "Taxonomy",
"GBSeq_create-date": "Create date",
"GBSeq_moltype": "Molecular type",
"GBSeq_topology": "Topology",
"GBSeq_references": "References",
"GBSeq_source": "Source",
"GBSeq_keywords": "Keywords",
"GBSeq_project": "Project",
"GBSeq_other-seqids": "Other IDs",
"GBSeq_strandedness": "Strandedness",
"GBSeq_comment": "Comments"
}
self.init_list()
self.updateSig.connect(self.updateTable)
self.searchSig.connect(self.ctrlSearchState)
self.progressBarSig.connect(self.searchProgress)
self.progressDiologSig.connect(self.runProgressDialog)
self.spinBox.valueChanged.connect(self.sync_display_items)
self.ctrlItemsSig.connect(self.ctrlItems)
# self.downloadFinished.connect(self.downloadDone)
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
self.NCBI_model = MyNCBITableModel([self.list_table_header],
parent=self)
self.tableView.setModel(self.NCBI_model)
header = CheckBoxHeader(parent=self.tableView)
header.clicked.connect(self.check_displayed)
self.tableView.setHorizontalHeader(header)
self.NCBI_model.checkedChanged.connect(self.ctrl_text)
self.interrupt = False
##下载的状态
widget = QWidget(self)
horizBox = QHBoxLayout(widget)
horizBox.setContentsMargins(0, 0, 0, 0)
spacerItem = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.disp_check_label = QLabel(
"<span style='font-weight:600; color:red;'>Searching...</span>",
self)
self.disp_check_gifLabel = QLabel(self)
movie = QMovie(":/picture/resourses/Spinner-1s-34px.gif")
self.disp_check_gifLabel.setMovie(movie)
self.disp_check_progress = QProgressBar(self)
self.disp_check_progress.setFixedWidth(100)
movie.start()
horizBox.addItem(spacerItem)
horizBox.addWidget(self.disp_check_gifLabel)
horizBox.addWidget(self.disp_check_label)
horizBox.addWidget(self.disp_check_progress)
self.statusbar.addPermanentWidget(widget)
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.installEventFilter(self)
self.spinBox.installEventFilter(self)
table_popMenu = QMenu(self)
table_popMenu.setToolTipsVisible(True)
OpenID = QAction(QIcon(":/seq_Viewer/resourses/field-Display.png"),
"Open in NCBI webpage",
self,
triggered=self.openID)
OpenID.setToolTip("Open sequence in NCBI webpage")
table_popMenu.addAction(OpenID)
def table_popmenu(qpoint):
if self.tableView.indexAt(qpoint).isValid():
table_popMenu.exec_(QCursor.pos())
self.tableView.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableView.customContextMenuRequested.connect(table_popmenu)
# self.tableView.horizontalHeader().resizeSection(1, 300)
# self.tableView.horizontalHeader().resizeSection(2, 80)
# ##增加check按钮
# self.check_all = QCheckBox("Check/Uncheck", self)
# self.check_all.toggled.connect(self.check_displayed)
# self.statusbar.addWidget(self.check_all)
## brief demo
self.label_6.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-3-1-Brief-example"
)))
@pyqtSlot()
def on_toolButton_clicked(self):
info = '''To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request.<br>
In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities.'''
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>%s</p>" % info)
@pyqtSlot()
def on_toolButton_2_clicked(self):
#refresh
self.interrupt = False
self.exist_base = self.NCBI_model.rowCount(self.tableView)
if not self.exist_base:
return
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
return
if self.display_items > self.exist_base:
self.worker_addition = WorkThread(self.addition_search,
parent=self)
self.worker_addition.start()
# elif self.display_items < self.exist_base:
# list_checked = self.NCBI_model.list_checked
# array = self.NCBI_model.array[:self.display_items+1]
# self.NCBI_model = MyNCBITableModel(array, list_checked, self.tableView)
# self.tableView.setModel(self.NCBI_model)
# self.tableView.update()
@pyqtSlot()
def on_toolButton_3_clicked(self):
# download
index = self.comboBox.currentIndex()
self.outputPath = self.comboBox.itemData(index, role=Qt.ToolTipRole)
self.rettype = "gb" if self.parent.isWorkFolder(self.outputPath,
mode="gb") else "fasta"
if self.rettype == "fasta":
name, ok = QInputDialog.getText(self,
'Set output file name',
'Output file name:',
text="sequence.fas")
if ok:
self.fasta_file_name = name + ".fas" if "." not in name else name
if os.path.exists(self.outputPath + os.sep +
self.fasta_file_name):
reply = QMessageBox.question(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>The file exists, replace it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Cancel:
return
else:
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>Download canceled!</p>"
)
return
if self.NCBI_model.arraydata:
self.interrupt = False
self.progressDialog = self.factory.myProgressDialog(
"Please Wait", "Downloading...", parent=self)
self.progressDialog.show()
self.worker_download = WorkThread(self.downloadSeq, parent=self)
self.progressDialog.canceled.connect(lambda: [
setattr(self, "interrupt", True),
self.worker_download.stopWork(),
self.progressDialog.close()
])
self.worker_download.finished.connect(self.downloadDone)
self.worker_download.start()
else:
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>Please search first!</p>"
)
def downloadSeq(self):
try:
checked_ids = self.NCBI_model.list_checked
# if not checked_ids:
# checked_ids = self.NCBI_model.fetchAllIDs()
batch_size = 20
count = len(checked_ids) if checked_ids else self.count
self.download_contents = ""
for start in range(0, count, batch_size):
if self.interrupt:
return
end = min(count, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > count:
batch_size = count - start
if not checked_ids:
#下载所有序列的模式
fetch_handle = Entrez.efetch(db=self.database,
rettype=self.rettype,
retmode="text",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
else:
fetch_handle = Entrez.efetch(db=self.database,
rettype=self.rettype,
retmode="text",
retstart=start,
retmax=batch_size,
id=checked_ids)
self.download_contents += fetch_handle.read()
self.progressDiologSig.emit(end * 100 / count)
# index = self.comboBox.currentIndex()
# filepath = self.comboBox.itemData(index, role=Qt.ToolTipRole)
# self.downloadFinished.emit()
except:
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
def downloadDone(self):
self.progressDialog.close()
QMessageBox.information(
self, "Download finished",
"<p style='line-height:25px; height:25px'>Done! Back to home page to view them.</p>"
)
if self.rettype == "gb":
self.inputContentSig.emit(self.download_contents, self.outputPath)
else:
with open(self.outputPath + os.sep + self.fasta_file_name,
"w",
encoding="utf-8") as f:
f.write(self.download_contents)
self.fastaDownloadFinishedSig.emit(self.outputPath)
def startSearch(self):
if hasattr(self, "worker") and self.worker.isRunning():
return
if self.spinBox.value() == 0:
self.spinBox.setValue(20)
if self.lineEdit.text():
self.interrupt = False
self.NCBI_model.init_table() #刷新一下table（归零）
self.worker = WorkThread(self.search, parent=self)
self.worker.start()
else:
QMessageBox.information(
self, "Search in NCBI",
"<p style='line-height:25px; height:25px'>Please input keywords first!</p>"
)
def guiSave(self):
# Save geometry
self.serhNCBI_settings.setValue('size', self.size())
# self.serhNCBI_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
# text = obj.currentText()
# if text:
# allItems = [
# obj.itemText(i) for i in range(obj.count())]
# allItems.remove(text)
# sortItems = [text] + allItems
# self.serhNCBI_settings.setValue(name, sortItems)
if isinstance(obj, QLineEdit):
if name == "lineEdit":
self.serhNCBI_settings.setValue(name, self.completer_texts)
if isinstance(obj, QSpinBox):
if name == "spinBox":
self.serhNCBI_settings.setValue(name, self.display_items)
def guiRestore(self):
# Restore geometry
self.resize(self.serhNCBI_settings.value('size', QSize(1000, 600)))
self.factory.centerWindow(self)
# self.move(self.serhNCBI_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox":
allItems = self.factory.fetchAllWorkFolders(self.workPath)
model = obj.model()
obj.clear()
for num, i in enumerate(allItems):
if self.parent.isWorkFolder(i, mode="gb"):
text = "\"%s\" in GenBank_File (GenBank format)" % os.path.basename(
i)
else:
text = "\"%s\" in Other_File (Fasta format)" % os.path.basename(
i)
item = QStandardItem(text)
item.setToolTip(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.setCurrentText(os.path.basename(self.workPath))
if self.parent.isWorkFolder(self.workPath, mode="gb"):
obj.setCurrentText(
"\"%s\" in GenBank_File (GenBank format)" %
os.path.basename(self.workPath))
else:
obj.setCurrentText(
"\"%s\" in Other_File (Fasta format)" %
os.path.basename(self.workPath))
if isinstance(obj, QLineEdit):
if name == "lineEdit":
self.completer_texts = self.serhNCBI_settings.value(
name, []) # get stored value from registry
self.setLCompleter()
if isinstance(obj, QSpinBox):
if name == "spinBox":
self.display_items = int(
self.serhNCBI_settings.value(
name, 100)) # get stored value from registry
obj.setValue(self.display_items)
def runProgressDialog(self, num):
oldValue = self.progressDialog.value()
done_int = int(num)
if done_int > oldValue:
self.progressDialog.setProperty("value", done_int)
QCoreApplication.processEvents()
if done_int == 100:
self.progressDialog.close()
def popupException(self, exception):
if ("getaddrinfo failed" in exception) or ("RuntimeError"
in exception):
text = "<p style='line-height:25px; height:25px'>Search failed, try to check your network connection!</p>"
else:
text = "<p style='line-height:25px; height:25px'>The search failed for some of the sequences. As this may have been caused by a network problem, you can wait for a while and try again.<br> If the problem persists you may report it 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]</p>"
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(text)
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def closeEvent(self, event):
self.interrupt = True
if hasattr(self, "worker") and self.worker.isRunning():
self.worker.stopWork()
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
self.worker_addition.stopWork()
if hasattr(self,
"worker_download") and self.worker_download.isRunning():
self.worker_download.stopWork()
if hasattr(self, "progressDialog"):
self.progressDialog.close()
self.guiSave()
# self.log_gui.close() # 关闭子窗口
def eventFilter(self, obj, event):
name = obj.objectName()
if event.type() == QEvent.KeyPress: # 首先得判断type
if event.key() == Qt.Key_Return:
if name == "lineEdit":
self.sync_completer_texts(self.lineEdit.text())
self.startSearch()
return True
if name == "spinBox":
self.on_toolButton_2_clicked()
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(SerhNCBI, self).eventFilter(obj, event) # 0
def sync_completer_texts(self, text):
if text and (text not in self.completer_texts):
self.completer_texts.insert(0, text)
if len(self.completer_texts) > 15:
self.completer_texts = self.completer_texts[:15]
self.guiSave()
self.setLCompleter()
def setLCompleter(self):
comp = QCompleter(self.completer_texts)
comp.setFilterMode(Qt.MatchContains)
comp.setCompletionMode(QCompleter.UnfilteredPopupCompletion)
# comp.popup().setStyleSheet("background-color: yellow")
self.lineEdit.setCompleter(comp)
def init_list(self):
self.list_table_header = [
"ID", "Description", "Organism", "Length", "Update date",
"Taxonomy", "Create date", "Molecular type", "Topology",
"References", "Source", "Keywords", "Project", "Other IDs",
"Strandedness", "Comments"
]
def updateTable(self, list_):
# print(array)
# 测试array是新添加的list
self.NCBI_model.appendTable(list_)
def ctrlSearchState(self, state):
if state == "searching":
self.disp_check_label.setText("Searching...")
self.disp_check_label.setVisible(True)
self.disp_check_gifLabel.setVisible(True)
self.lineEdit.buttonSearch.setDisabled(True)
self.lineEdit.buttonStop.setDisabled(False)
self.toolButton_2.setDisabled(True)
self.toolButton_3.setDisabled(True)
elif state == "fetching":
self.disp_check_label.setText("Fetching...")
self.disp_check_label.setVisible(True)
self.disp_check_gifLabel.setVisible(True)
self.disp_check_progress.setValue(0)
self.disp_check_progress.setVisible(True)
self.lineEdit.buttonStop.setDisabled(False)
elif state == "except":
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.buttonSearch.setDisabled(False)
self.lineEdit.buttonStop.setDisabled(True)
self.toolButton_2.setDisabled(False)
self.toolButton_3.setDisabled(False)
elif state == "finished":
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.buttonSearch.setDisabled(False)
self.lineEdit.buttonStop.setDisabled(True)
self.toolButton_2.setDisabled(False)
self.toolButton_3.setDisabled(False)
##如果啥也没搜到
self.exist_base = self.NCBI_model.rowCount(self.tableView)
if not self.exist_base:
QMessageBox.information(
self, "Download finished",
"<p style='line-height:25px; height:25px'>No items found!</p>"
)
def ctrlItems(self, count):
count = count if count != 0 else 20
self.spinBox.setMaximum(count)
if count == 0:
self.spinBox.setValue(20)
self.label_4.setText("items of %s (total)" % count)
self.label_2.setText("Download all (%s) sequences to:" % count)
# if count < self.display_items:
# self.display_items = count
# self.spinBox.setValue(count)
def searchProgress(self, value):
oldValue = self.disp_check_progress.value()
done_int = int(value)
if done_int > oldValue:
self.disp_check_progress.setProperty("value", done_int)
QCoreApplication.processEvents()
def sync_display_items(self, value):
self.display_items = value
def search(self):
try:
self.searchSig.emit("searching")
self.init_list()
self.ctrl_text() #文本还原
self.NCBI_model.list_checked = []
self.database = self.comboBox_2.currentText()
keywords = self.lineEdit.text()
email = self.lineEdit_2.text()
email = email if email else "*****@*****.**"
Entrez.email = email
search_handle = Entrez.esearch(db=self.database,
term=keywords,
usehistory="y")
search_results = Entrez.read(search_handle)
self.webenv = search_results["WebEnv"]
self.query_key = search_results["QueryKey"]
self.count = int(search_results["Count"])
self.ctrlItemsSig.emit(
self.count) #如果只有2个序列，self.display_items也会变成2
search_handle.close()
batch_size = 20
self.searchSig.emit("fetching")
# time_start = time.time()
total_displayed = self.display_items
if self.count < total_displayed:
total_displayed = self.count
for start in range(0, total_displayed, batch_size):
# try:
if self.interrupt:
return
end = min(total_displayed, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > total_displayed:
batch_size = total_displayed - start
fetch_handle = Entrez.efetch(db=self.database,
retmode="xml",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
fetch_records = Entrez.read(fetch_handle)
for num, record in enumerate(fetch_records):
list_ = []
for i in [
"GBSeq_accession-version", "GBSeq_definition",
"GBSeq_organism", "GBSeq_length",
"GBSeq_update-date", "GBSeq_taxonomy",
"GBSeq_create-date", "GBSeq_moltype",
"GBSeq_topology", "GBSeq_references",
"GBSeq_source", "GBSeq_keywords", "GBSeq_project",
"GBSeq_other-seqids", "GBSeq_strandedness",
"GBSeq_comment"
]:
if i in record:
list_.append(str(record[i]))
else:
list_.append("N/A")
self.updateSig.emit(list_)
self.progressBarSig.emit(
(start + num + 1) * 100 / total_displayed)
fetch_handle.close()
# except:
# pass
self.searchSig.emit("finished")
except:
self.searchSig.emit("except")
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
# time_end = time.time()
# print("time:", time_end - time_start)
def addition_search(self):
try:
total_displayed = self.display_items
if self.count < total_displayed:
total_displayed = self.count
batch_size = 20
self.searchSig.emit("fetching")
for start in range(self.exist_base, total_displayed, batch_size):
if self.interrupt:
break
end = min(total_displayed, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > total_displayed:
batch_size = total_displayed - start
fetch_handle = Entrez.efetch(db=self.database,
retmode="xml",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
fetch_records = Entrez.read(fetch_handle)
for num, record in enumerate(fetch_records):
list_ = []
for i in [
"GBSeq_accession-version", "GBSeq_definition",
"GBSeq_organism", "GBSeq_length",
"GBSeq_update-date", "GBSeq_taxonomy",
"GBSeq_create-date", "GBSeq_moltype",
"GBSeq_topology", "GBSeq_references",
"GBSeq_source", "GBSeq_keywords", "GBSeq_project",
"GBSeq_other-seqids", "GBSeq_strandedness",
"GBSeq_comment"
]:
if i in record:
list_.append(str(record[i]))
else:
list_.append("N/A")
self.updateSig.emit(list_)
self.progressBarSig.emit(
(start - self.exist_base + num + 1) * 100 /
(total_displayed - self.exist_base))
# self.progressBarSig.emit((start - self.exist_base)*100/(total_displayed - self.exist_base))
fetch_handle.close()
self.searchSig.emit("finished")
except:
self.searchSig.emit("except")
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
def ctrl_text(self):
selected_num = len(self.NCBI_model.list_checked)
if selected_num:
self.label_2.setText("Download selected (%d) sequences to:" %
(selected_num))
else:
text = "Download all (%d) sequences to:" % self.count if hasattr(
self, "count") else "Download all sequences to:"
self.label_2.setText(text)
def openID(self):
indices = self.tableView.selectedIndexes()
arraydata = self.NCBI_model.arraydata
ID = arraydata[indices[0].row()][0].text()
url = "https://www.ncbi.nlm.nih.gov/nuccore/%s"%ID if self.comboBox_2.currentText() == "nucleotide" \
else "https://www.ncbi.nlm.nih.gov/protein/%s"%ID
QDesktopServices.openUrl(QUrl(url))
def stopSearch(self):
self.interrupt = True
if hasattr(self, "worker") and self.worker.isRunning():
self.worker.stopWork()
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
self.worker_addition.stopWork()
self.searchSig.emit("except")
def check_displayed(self, isCheck):
if hasattr(self, "NCBI_model") and self.NCBI_model.rowCount(
self.tableView):
# self.NCBI_model.beginResetModel()
self.NCBI_model.layoutAboutToBeChanged.emit()
if isCheck:
self.NCBI_model.list_checked = [
i[0].text() for i in self.NCBI_model.arraydata
]
else:
self.NCBI_model.list_checked = []
self.NCBI_model.layoutChanged.emit()
self.ctrl_text()
class DrawRSCUfig(QDialog, Ui_RSCUfig, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
warning_signal = pyqtSignal(str)
progressSig = pyqtSignal(int) # 控制进度条
startButtonStatusSig = pyqtSignal(list)
def __init__(self,
autoInputs=None,
workPath=None,
focusSig=None,
RscriptPath=None,
parent=None):
super(DrawRSCUfig, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoInputs = autoInputs
self.RscriptPath = RscriptPath
self.setupUi(self)
# 保存设置
self.DrawRSCUfig_settings = QSettings(
self.thisPath + '/settings/DrawRSCUfig_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.DrawRSCUfig_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.warning_signal.connect(self.popupWarning)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.listWidget_3.installEventFilter(self)
# 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_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-14-3-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
open files
"""
fileNames = QFileDialog.getOpenFileNames(self,
"Input Files",
filter="CSV Format(*.csv);;")
if fileNames[0]:
dict_inputs = OrderedDict()
for i in fileNames[0]:
dict_inputs[i] = os.path.splitext(os.path.basename(i))[0]
self.inputListWidget_3(dict_inputs)
@pyqtSlot()
def on_toolButton_T_clicked(self):
'''
delete
'''
listItems = self.listWidget_3.selectedItems()
if not listItems:
return
for item in listItems:
self.listWidget_3.takeItem(self.listWidget_3.row(item))
@pyqtSlot()
def on_pushButton_2_clicked(self):
'''
cancel
'''
# ctypes.windll.kernel32.TerminateThread( # @UndefinedVariable
# self.worker.handle, 0)
self.close()
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
dict_inputs = OrderedDict()
for i in range(self.listWidget_3.count()):
dict_inputs[self.listWidget_3.item(
i).toolTip()] = self.listWidget_3.item(i).text()
if dict_inputs:
# 有数据才执行
self.dict_args = {}
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + os.sep +
"RSCUfig_results" +
os.sep +
self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
self.dict_args["dict_files_title"] = dict_inputs
self.dict_args["exception_signal"] = self.exception_signal
self.dict_args["progressSig"] = self.progressSig
xItems = [
self.listWidget_2.item(i).text()
for i in range(self.listWidget_2.count())
]
self.dict_args["Order of x-axis"] = xItems
colorItems = [
i.text() for i in [
self.pushButton_color, self.pushButton_color_2,
self.pushButton_color_3, self.pushButton_color_4
]
]
self.dict_args["Color of stacks"] = colorItems
self.dict_args["Figure height"] = self.spinBox_5.value()
self.dict_args["Figure width"] = self.spinBox_6.value()
self.dict_args["height proportion"] = self.doubleSpinBox_2.value()
self.dict_args["ylim"] = self.doubleSpinBox_3.value()
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
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.critical(
self, "Draw RSCU figure",
"<p style='line-height:25px; height:25px'>Please input files first!</p>"
)
def run_command(self):
try:
# 清空文件夹，放在这里方便统一报错
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start", self.exportPath,
self.qss_file, self
])
rscriptPath = self.rscu2fig()
# subprocess.call([self.RscriptPath, "--vanilla", rscriptPath], shell=True)
subprocess.call("%s --vanilla %s" %
(self.RscriptPath, rscriptPath),
shell=True)
self.progressSig.emit(100)
if not os.path.exists(self.RSCUpath):
self.warning_signal.emit(
"No RSCU figure generated! The R packages \"ggplot2\" or \"ggpubr\" may not be installed properly. You may:<br>"
" <span style='font-weight:600'>1</span>. Install \"ggplot2\" and \"ggpubr\" manually, restart PhyloSuite and try again<br>"
" <span style='font-weight:600'>2</span>. Execute \"rscu_scripts.r\" script: <span style='font-weight:600; color:#ff0000;'>Rscript rscu_scripts.r</span><br>"
" <span style='font-weight:600'>3</span>. Copy the content of \"rscu_scripts.r\" and paste it into Rstudio or Rgui to execute"
)
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.exportPath, self.qss_file, self
])
else:
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "stop", self.exportPath,
self.qss_file, self
])
if os.path.exists(self.exportPath + os.sep + "Rplots.pdf"):
os.remove(self.exportPath + os.sep + "Rplots.pdf")
self.focusSig.emit(self.exportPath)
time_end = datetime.datetime.now()
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (
str(time_start), str(time_end), str(time_end - time_start))
with open(self.exportPath + os.sep + "summary.txt",
"w",
encoding="utf-8") as f:
f.write(
"If 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\n"
+ self.time_used_des)
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.DrawRSCUfig_settings.setValue('size', self.size())
# self.DrawRSCUfig_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, QListWidget):
if name == "listWidget_3":
dict_inputs = OrderedDict()
for i in range(obj.count()):
dict_inputs[obj.item(i).toolTip()] = obj.item(i).text()
self.DrawRSCUfig_settings.setValue(name, dict_inputs)
else:
allItems = [obj.item(i).text() for i in range(obj.count())]
self.DrawRSCUfig_settings.setValue(name, allItems)
if isinstance(obj, QSpinBox):
value = obj.value()
self.DrawRSCUfig_settings.setValue(name, value)
if isinstance(obj, QDoubleSpinBox):
value = obj.value()
self.DrawRSCUfig_settings.setValue(name, value)
if isinstance(obj, QPushButton):
if name in [
"pushButton_color", "pushButton_color_2",
"pushButton_color_3", "pushButton_color_4"
]:
color = obj.palette().color(1)
self.DrawRSCUfig_settings.setValue(name, color.name())
def guiRestore(self):
# Restore geometry
self.resize(self.DrawRSCUfig_settings.value('size', QSize(500, 500)))
self.factory.centerWindow(self)
# self.move(self.DrawRSCUfig_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QListWidget):
if name == "listWidget_2":
ini_list = [
"Gln", "His", "Asn", "Pro", "Thr", "Leu1", "Glu",
"Met", "Arg", "Tyr", "Asp", "Lys", "Ala", "Ile",
"Ser1", "Ser2", "Leu2", "Cys", "Trp", "Val", "Gly",
"Phe"
]
values = self.DrawRSCUfig_settings.value(name, ini_list)
self.inputListWidget(values, obj)
elif name == "listWidget_3":
ini_dict_input = OrderedDict()
dict_inputs = self.DrawRSCUfig_settings.value(
name, ini_dict_input)
if self.autoInputs:
dict_inputs = OrderedDict()
for i in self.autoInputs:
dict_inputs[i] = os.path.splitext(
os.path.basename(i))[0]
self.inputListWidget_3(dict_inputs)
if isinstance(obj, QSpinBox):
value = self.DrawRSCUfig_settings.value(name, 8)
obj.setValue(int(value))
if isinstance(obj, QDoubleSpinBox):
value = self.DrawRSCUfig_settings.value(name, None)
if value:
obj.setValue(float(value))
if isinstance(obj, QPushButton):
if obj in [
self.pushButton_color, self.pushButton_color_2,
self.pushButton_color_3, self.pushButton_color_4
]:
dict_ini_colors = {
"pushButton_color": "#6598C9",
"pushButton_color_2": "#CB4A28",
"pushButton_color_3": "#9AC664",
"pushButton_color_4": "#7F5499"
}
ini_color = dict_ini_colors[name]
color = self.DrawRSCUfig_settings.value(name, ini_color)
obj.setStyleSheet("background-color:%s" % color)
obj.setText(color)
obj.clicked.connect(self.changePbColor)
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):
rgx = re.compile(r'Permission.+?[\'\"](.+\.pdf)[\'\"]')
if rgx.search(exception):
pdffile = rgx.search(exception).group(1)
reply = QMessageBox.critical(
self, "Draw RSCU figure",
"<p style='line-height:25px; height:25px'>Please close 'pdf' file first!</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes and platform.system().lower(
) == "windows":
os.startfile(pdffile)
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 closeEvent(self, event):
self.guiSave()
def inputListWidget(self, items, listwidget):
listwidget.clear()
for num, i in enumerate(items):
item = QListWidgetItem(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
listwidget.addItem(item)
def inputListWidget_3(self, dict_items):
if not dict_items:
return
self.listWidget_3.clear()
for num, i in enumerate(dict_items):
if os.path.exists(i):
item = QListWidgetItem(dict_items[i])
item.setToolTip(i)
item.setFlags(item.flags() | Qt.ItemIsEditable)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
self.listWidget_3.addItem(item)
def rscu2fig(self):
script = '''# auto install missing packages
list.of.packages <- c("ggplot2", "ggpubr")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages, repos="http://cran.us.r-project.org")
library("ggplot2")
scaleFUN <- function(x) sprintf("%.2f", x) #可以设置坐标轴显示的小数点位数，为了与图注保持一致\n'''
allfig = [] # [1,2,3,4]
sums = len(self.dict_args["dict_files_title"])
for num, i in enumerate(self.dict_args["dict_files_title"]):
self.Order_name = self.factory.int2word(num + 1).strip().replace(
" ", "_")
self.rscu_file = os.path.normpath(i).replace("\\", "/")
self.latin_name = self.dict_args["dict_files_title"][i]
self.spe_number = str(num + 1)
allfig.append(self.spe_number)
self.Xaxis = '"' + '","'.join(
self.dict_args["Order of x-axis"]) + '"'
self.ylim = "%.1f" % self.dict_args["ylim"]
# 生成RSCU堆积条形图代码
script_i = '''
{self.Order_name} <- read.table("{self.rscu_file}",header = TRUE,sep=",")
f{self.Order_name} <- factor({self.Order_name}$Fill, levels = unique(rev({self.Order_name}$Fill))) #填充的颜色的factor
#自定义横坐标顺序
x{self.Order_name} <- factor({self.Order_name}$AA, levels=c({self.Xaxis})) #横坐标
y{self.Order_name} <- {self.Order_name}$RSCU #Y值
z{self.Order_name} <- {self.Order_name}$Equality #图注的Y值
l{self.Order_name} <- {self.Order_name}$Codon #图注打标签
p{self.spe_number} <- ggplot(data = {self.Order_name}, mapping = aes(x = x{self.Order_name}, y = y{self.Order_name}, fill = f{self.Order_name},width = .7)) + geom_bar(stat = 'identity', position = 'stack')+ ggtitle("{self.latin_name}")+theme(axis.title.x=element_blank(),axis.title.y=element_text(size=10),legend.position="none",panel.background=element_blank(),panel.grid.minor=element_blank(),plot.background=element_blank(),axis.line.x = element_line(color="black", size = 0.5),axis.line.y = element_line(color="black", size = 0.5),axis.text.x=element_blank(), plot.title=element_text(family="sans",face="italic",hjust=0,size=10)) + scale_fill_manual("legend", values = c("1" = "{self.dict_args[Color of stacks][0]}", "2" = "{self.dict_args[Color of stacks][1]}", "3" = "{self.dict_args[Color of stacks][2]}", "4" = "{self.dict_args[Color of stacks][3]}"))+geom_text(mapping = aes(label = factor({self.Order_name}$aaRatio)), size = 2.5, vjust=-.2,position = position_stack()) + ylim(0,{self.ylim})+ylab("RSCU")\n'''.format(
self=self)
if num == (len(self.dict_args["dict_files_title"]) - 1):
#最后一个要添加横坐标
script_i = script_i.replace("axis.text.x=element_blank(),", "")
script += script_i
if num == 0:
bottom = '''
p <- ggplot(data = {self.Order_name}, mapping = aes(x = x{self.Order_name}, y = z{self.Order_name}, fill = f{self.Order_name},width = .9)) + geom_bar(stat = 'identity', position = 'stack') + geom_text(mapping = aes(label = l{self.Order_name}), size = 2.4, colour = 'white', position = position_stack(vjust=.5))+theme(axis.text.x=element_blank(),axis.text.y=element_blank(),axis.ticks=element_blank(),axis.title.x=element_blank(),axis.title.y=element_blank(),legend.position="none",panel.background=element_blank(),panel.border=element_blank(),panel.grid.major=element_blank(),panel.grid.minor=element_blank(),plot.background=element_blank(),axis.line.y = element_blank()) + scale_fill_manual("legend", values = c("1" = "{self.dict_args[Color of stacks][0]}", "2" = "{self.dict_args[Color of stacks][1]}", "3" = "{self.dict_args[Color of stacks][2]}", "4" = "{self.dict_args[Color of stacks][3]}"))\n'''.format(
self=self)
self.progressSig.emit((num + 1) * 50 / sums)
script += bottom
allfig.append("")
self.allfignum = "p" + ",p".join(allfig)
self.str_matrix = ",".join(
["1"] * len(self.dict_args["dict_files_title"]) +
["%.2f" %
(1 / self.dict_args["height proportion"])]) # (1,1,1,0.5)
self.nrow = str(len(self.dict_args["dict_files_title"]) + 1)
self.RSCUpath = os.path.normpath(self.exportPath + os.sep +
"RSCU.pdf").replace("\\", "/")
script += '''
library("ggpubr")
pall <- ggarrange({self.allfignum}, heights=c({self.str_matrix}), ncol=1, nrow={self.nrow}, align ="v")
pdf("{self.RSCUpath}",width={self.dict_args[Figure width]},height={self.dict_args[Figure height]}) ## 如果觉得比例不合适，可以适当调整width和height的大小。
pall
dev.off()
'''.format(self=self)
scriptPath = self.exportPath + os.sep + "rscu_scripts.r"
with open(scriptPath, "w", encoding="utf-8") as f:
f.write(script)
self.progressSig.emit(60)
return scriptPath
def changePbColor(self):
button = self.sender()
ini_color = button.palette().color(1)
color = QColorDialog.getColor(QColor(ini_color), self)
if color.isValid():
button.setText(color.name())
button.setStyleSheet("background-color:%s" % color.name())
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
if isinstance(obj, QListWidget):
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()]
dict_inputs = {}
for i in files:
dict_inputs[i] = os.path.splitext(os.path.basename(i))[0]
self.inputListWidget_3(dict_inputs)
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
# 其他情况会返回系统默认的事件处理方法。
return super(DrawRSCUfig, self).eventFilter(obj, event) # 0
def popupWarning(self, text):
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
class CompareTable(QDialog, Ui_compareTable, 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)
def __init__(self,
autoInputs=None,
workPath=None,
focusSig=None,
MAFFTpath=None,
parent=None):
super(CompareTable, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.mafft_exe = MAFFTpath
self.setupUi(self)
self.autoInputs = autoInputs
self.focusSig = focusSig
# 保存设置
self.CompareTable_settings = QSettings(
self.thisPath + '/settings/CompareTable_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.CompareTable_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.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.listWidget.installEventFilter(self)
# 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_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-14-2-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
self.list_files = [
self.listWidget.item(i).toolTip()
for i in range(self.listWidget.count())
]
if len(self.list_files) >= 2:
# 有数据才执行
self.headerRows = self.spinBox.value()
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + os.sep +
"comp_tbl_results" +
os.sep +
self.output_dir_name)
self.ispairwiseAlign = self.checkBox.isChecked()
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
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.critical(
self, "Compare table",
"<p style='line-height:25px; height:25px'>Please input at least two files!</p>"
)
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
open files
"""
fileNames = QFileDialog.getOpenFileNames(self,
"Input Files",
filter="CSV Format(*.csv);;")
if fileNames[0]:
self.input(fileNames[0])
@pyqtSlot()
def on_toolButton_T_clicked(self):
'''
delete
'''
listItems = self.listWidget.selectedItems()
if not listItems:
return
for item in listItems:
self.listWidget.takeItem(self.listWidget.row(item))
@pyqtSlot()
def on_pushButton_2_clicked(self):
'''
cancel
'''
# ctypes.windll.kernel32.TerminateThread( # @UndefinedVariable
# self.worker.handle, 0)
self.close()
def run_command(self):
try:
#清空文件夹，放在这里方便统一报错
time_start = datetime.datetime.now()
# raise BaseException
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start", self.exportPath,
self.qss_file, self
])
self.gatherTable = GatherTable(self.list_files,
self.ispairwiseAlign,
self.exportPath, self.progressSig,
self.mafft_exe, self.headerRows)
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "stop", self.exportPath,
self.qss_file, self
])
self.focusSig.emit(self.exportPath)
time_end = datetime.datetime.now()
description = """The sequences were pairwise aligned with MAFFT (Katoh and Standley, 2013) first, then the genetic distances (identity) among sequences were calculated with the “DistanceCalculator” function in Biopython (C**k, et al., 2009) using the “identity” model."""
mafft_ref = "Katoh, K., Standley, D.M., 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780."
biopython_ref = "C**k, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422-1423."
self.time_used_des = "Start at: %s\nFinish at: %s\nTotal time used: %s\n\n" % (
str(time_start), str(time_end), str(time_end - time_start))
ps_cite = "If you use PhyloSuite, please cite:\nZhang, D., Gao, F., Li, W.X., Jakovlić, I., Zou, H., Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. bioRxiv, doi: 10.1101/489088.\n\n"
text = ps_cite + self.time_used_des if not self.checkBox.isChecked(
) else description + "\n\n" + ps_cite + "If you use MAFFT, please cite:\n%s\n\nIf you use Biopython, please cite:\n%s\n\n" % (
mafft_ref, biopython_ref) + self.time_used_des
with open(self.exportPath + os.sep + "summary.txt",
"w",
encoding="utf-8") as f:
f.write(text)
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.CompareTable_settings.setValue('size', self.size())
# self.CompareTable_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, QListWidget):
allItems = [obj.item(i).toolTip() for i in range(obj.count())]
self.CompareTable_settings.setValue(name, allItems)
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.CompareTable_settings.setValue(name, state)
def guiRestore(self):
# Restore geometry
self.resize(self.CompareTable_settings.value('size', QSize(500, 500)))
# self.move(self.CompareTable_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QListWidget):
if self.autoInputs:
self.input(self.autoInputs)
else:
values = self.CompareTable_settings.value(name, [])
if values:
self.input(values)
if isinstance(obj, QCheckBox):
value = self.CompareTable_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):
rgx = re.compile(r'Permission.+?[\'\"](.+\.csv)[\'\"]')
if rgx.search(exception):
csvfile = rgx.search(exception).group(1)
reply = QMessageBox.critical(
self, "Compare table",
"<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 closeEvent(self, event):
self.guiSave()
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
if isinstance(obj, QListWidget):
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()]
self.input(files)
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
# 其他情况会返回系统默认的事件处理方法。
return super(CompareTable, self).eventFilter(obj, event) # 0
def input(self, files):
self.listWidget.clear()
for num, i in enumerate(files):
if not os.path.exists(i):
continue
item = QListWidgetItem(os.path.basename(i))
item.setToolTip(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
self.listWidget.addItem(item)
class HmmCleaner(QDialog, Ui_HmmCleaner, 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)
HmmCleaner_exception = pyqtSignal(str)
workflow_progress = pyqtSignal(int)
workflow_finished = pyqtSignal(str)
# 用于输入文件后判断用
ui_closeSig = pyqtSignal(str)
# 用于flowchart自动popup combobox等操作
showSig = pyqtSignal(QDialog)
closeSig = pyqtSignal(str, str)
def __init__(self,
workPath=None,
HmmCleanerPath=None,
autoInputs=None,
perl=None,
focusSig=None,
workflow=None,
parent=None):
super(HmmCleaner, self).__init__(parent)
self.parent = parent
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.autoInputs = autoInputs
self.HmmCleanerPath = HmmCleanerPath
self.perl = perl
self.setupUi(self)
# 保存设置
if not workflow:
self.HmmCleaner_settings = QSettings(
self.thisPath + '/settings/HmmCleaner_settings.ini',
QSettings.IniFormat)
else:
self.HmmCleaner_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.HmmCleaner_settings.beginGroup("Workflow")
self.HmmCleaner_settings.beginGroup("temporary")
self.HmmCleaner_settings.beginGroup('HmmCleaner')
# File only, no fallback to registry or or.
self.HmmCleaner_settings.setFallbacksEnabled(False)
# print(self.HmmCleaner_settings.childGroups())
# self.factory.settingsGroup2Group(self.HmmCleaner_settings, "PCGs", "temporary")
# 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.interrupt = False
self.exception_signal.connect(self.popupException)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
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.log_gui = self.gui4Log()
self.HmmCleaner_exception.connect(self.popup_HmmCleaner_exception)
self.checkBox_4.toggled.connect(self.popupAliWarning)
# 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_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-5-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
self.command = self.fetchCommands()
if self.command:
self.interrupt = False
self.error_has_shown = False # 保证只报一次错
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
thread = thread if len(
self.dict_args["inputFiles"]) > thread else len(
self.dict_args["inputFiles"])
thread = 1 if not self.dict_args[
"inputFiles"] else thread # compare的情况
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
show log
"""
self.log_gui.show()
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
alignment file
"""
fileNames = QFileDialog.getOpenFileNames(self, "Input alignment file")
if fileNames[0]:
self.input(fileNames[0])
@pyqtSlot()
def on_pushButton_2_clicked(self, quiet=False):
"""
Stop
"""
if self.isRunning():
if (not self.workflow) and (not quiet):
reply = QMessageBox.question(
self, "Confirmation",
"<p style='line-height:25px; height:25px'>HmmCleaner is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
else:
reply = QMessageBox.Yes
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
if (not self.workflow) and (not quiet):
QMessageBox.information(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>Program has been terminated!</p>"
)
self.startButtonStatusSig.emit([
self.pushButton, [self.progressBar], "except",
self.dict_args["exportPath"], self.qss_file, self
])
def run_command(self):
try:
# 清空文件夹，放在这里方便统一报错
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start",
self.dict_args["exportPath"], self.qss_file, self
])
##进度条用
# self.dict_file_progress = {os.path.basename(file): 0 for file in self.dict_args["seq_files"]}
async_results = [
self.pool.apply_async(run,
args=(self.dict_args, self.command,
file))
for file in self.dict_args["inputFiles"]
]
self.totalFileNum = len(self.dict_args["inputFiles"])
self.finishedFileNum = 0 #进度条用
self.pool.close() # 关闭进程池，防止进一步操作。如果所有操作持续挂起，它们将在工作进程终止前完成
map(ApplyResult.wait, async_results)
lst_results = [r.get() for r in async_results]
# 判断比对是否成功
HmmCleaner_results = glob.glob(self.exportPath + os.sep +
"*_hmm.*")
empty_files = [
os.path.basename(file) for file in HmmCleaner_results
if os.stat(file).st_size == 0
]
has_error = False
if (not self.checkBox_3.isChecked()) and (not HmmCleaner_results
or empty_files):
# log_only不管
has_error = True
log = self.textEdit_log.toPlainText()
if "Can't locate" in log:
self.HmmCleaner_exception.emit(
"HmmCleaner executes failed, it seems the "
"<a href=\"https://cpandeps.grinnz.com/?dist=Bio-MUST-Apps-HmmCleaner&phase=build&perl_version=v5.30.0&style=table\">"
"<span style=\" font-size:12pt; text-decoration: underline; color:#0000ff;\">dependencies"
"</span></a>(e.g. Bio-FastParsers) of HmmCleaner are not installed, "
"click <span style=\"color:red\">Show log</span> to see details! <br> You can install HmmCleaner following this " \
"<a href=\"https://dongzhang0725.github.io/dongzhang0725.github.io/PhyloSuite-demo/how-to-configure-plugins/#2-4-HmmCleaner-configuration\">" \
"<span style=\" font-size:12pt; text-decoration: underline; color:#0000ff;\">instruction</a>." \
"</span>")
else:
list_commands = re.findall(r"Command: (.+)\n", log)
last_cmd = list_commands[-1] if list_commands else ""
self.HmmCleaner_exception.emit(
"HmmCleaner executes failed, click <span style=\"color:red\">Show log</span> to see details! "
"You can also copy this command to terminal to debug: %s"
% last_cmd)
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., Gao, F., Li, W.X., Jakovlić, I., Zou, H., Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. bioRxiv, doi: 10.1101/489088.\n"
"If you use HmmCleaner, please cite:\n" + self.reference +
"\n\n" + self.time_used_des)
if (not self.interrupt) and (not has_error):
self.pool = None
self.interrupt = False
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
])
self.pool = None
self.interrupt = False
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.dict_args["exportPath"], self.qss_file, self
])
self.pool = None
self.interrupt = False
def guiSave(self):
# Save geometry
self.HmmCleaner_settings.setValue('size', self.size())
# self.HmmCleaner_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.HmmCleaner_settings.setValue(name, index)
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.HmmCleaner_settings.setValue(name, state)
elif isinstance(obj, QDoubleSpinBox):
float_ = obj.value()
self.HmmCleaner_settings.setValue(name, float_)
def guiRestore(self):
# Restore geometry
self.resize(self.HmmCleaner_settings.value('size', QSize(490, 380)))
# self.move(self.HmmCleaner_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 = [str(i + 1) for i in range(cpu_num)]
index = self.HmmCleaner_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))
elif name == "comboBox_4":
self.input(self.autoInputs)
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
index = self.HmmCleaner_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))
item.setToolTip(i)
model.appendRow(item)
obj.setCurrentIndex(int(index))
elif isinstance(obj, QCheckBox):
value = self.HmmCleaner_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
elif isinstance(obj, QDoubleSpinBox):
ini_float_ = obj.value()
float_ = self.HmmCleaner_settings.value(name, ini_float_)
obj.setValue(float(float_))
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("HmmCleaner", 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("HmmCleaner")
# 自动跑的时候不杀掉程序
return
if self.isRunning():
reply = QMessageBox.question(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>HmmCleaner is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
else:
event.ignore()
def showEvent(self, event):
QTimer.singleShot(100, lambda: self.showSig.emit(self))
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()]
self.input(files)
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(HmmCleaner, 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 HmmCleaner:")
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)
def save_log_to_file(self):
content = self.textEdit_log.toPlainText()
fileName = QFileDialog.getSaveFileName(self, "HmmCleaner", "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 input(self, list_items=None):
if list_items:
self.comboBox_4.refreshInputs(list_items)
else:
self.comboBox_4.refreshInputs([])
def showCMD(self):
"""
show command
"""
self.command = self.fetchCommands()
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)
self.textEdit_cmd.textChanged.connect(self.judgeCmdText)
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 isRunning(self):
'''判断程序是否运行,依赖进程是否存在来判断'''
return hasattr(self, "pool") and self.pool and not self.interrupt
def run_with_CMD(self, cmd):
self.command = cmd
if self.command:
self.interrupt = False
self.error_has_shown = False
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
thread = thread if len(
self.dict_args["inputFiles"]) > thread else len(
self.dict_args["inputFiles"])
thread = 1 if not self.dict_args[
"inputFiles"] else thread # compare的情况
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# # Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
def judgeCmdText(self):
text = self.textEdit_cmd.toPlainText()
if " $alignment$" not in text:
QMessageBox.information(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>\"$alignment$\" cannot be changed!</p>"
)
self.textEdit_cmd.undo()
def fetchCommands(self):
if self.isFileIn():
self.interrupt = False
self.error_has_shown = False
self.dict_args = {}
self.dict_args["workPath"] = self.workPath
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + \
os.sep + "HmmCleaner_results" + os.sep + self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
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
costs = "\"%.2f\" \"%.2f\" \"%.2f\" \"%.2f\"" % (
self.doubleSpinBox.value(), self.doubleSpinBox_2.value(),
self.doubleSpinBox_3.value(), self.doubleSpinBox_4.value())
self.dict_args[
"costs"] = " -costs %s" % costs if costs != '"-0.15" "-0.08" "0.15" "0.45"' else ""
self.dict_args["noX"] = " --noX" if self.checkBox_5.isChecked(
) else ""
self.dict_args[
"specificity"] = " --specificity" if self.checkBox.isChecked(
) else ""
self.dict_args["large"] = " --large" if self.checkBox_2.isChecked(
) else ""
self.dict_args[
"log_only"] = " --log_only" if self.checkBox_3.isChecked(
) else ""
self.dict_args["ali"] = " --ali" if self.checkBox_4.isChecked(
) else ""
self.dict_args[
"changeID"] = " --changeID" if self.checkBox_6.isChecked(
) else ""
self.dict_args[
"profile"] = " -profile=%s" % self.comboBox_3.currentText()
self.dict_args[
"symfrac"] = " -symfrac %s" % self.doubleSpinBox_6.value(
) if self.doubleSpinBox_6.value() != 0.50 else ""
self.dict_args[
"verbosity"] = " -v=%s" % self.comboBox_5.currentText(
) if self.comboBox_5.currentText() != "0" else ""
self.dict_args[
"perl"] = "\"%s\" " % self.perl if self.HmmCleanerPath != "HmmCleaner.pl" else "" #如果是用的环境变量的脚本，就不用perl
self.dict_args["HmmCleaner"] = self.HmmCleanerPath
##输入文件
self.dict_args["inputFiles"] = []
try:
for aln_file in self.comboBox_4.fetchListsText():
with open(aln_file, encoding="utf-8",
errors="ignore") as f:
content = f.read()
copy_path = self.exportPath + os.sep + os.path.basename(
aln_file)
with open(copy_path, "w", encoding="utf-8") as f1:
f1.write(content.replace("\r\n", "\n"))
self.dict_args["inputFiles"].append(copy_path)
except:
QMessageBox.information(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>File copying failed, please check your input files!</p>"
)
command = "{perl}\"{HmmCleaner}\" $alignment${costs}{noX}{specificity}{large}{log_only}{ali}" \
"{changeID}{profile}{symfrac}{verbosity}".format(**self.dict_args)
self.reference = "Di Franco A, Poujol R, Baurain D, Philippe H. 2019. Evaluating the usefulness of " \
"alignment filtering methods to reduce the impact of errors on evolutionary " \
"inferences. BMC Evol Biol. 19: 21. doi: 10.1186/s12862-019-1350-2."
cmd_used = "{costs}{specificity}{large}{log_only}{ali}{changeID}{profile}{symfrac}".format(
**self.dict_args).strip()
self.description = "Low similarity segments within the alignment were removed with HmmCleaner (Di Franco et al., 2019) using \"%s\" command." % cmd_used
self.textEdit_log.clear() # 清空
return command
else:
QMessageBox.critical(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>Please input files first!</p>"
)
def updateProcess(self):
if self.queue.empty(): return
info = self.queue.get()
if info[0] == "log":
message = info[1]
self.logGuiSig.emit(message)
elif info[0] == "prog":
self.finishedFileNum += 1
if not self.interrupt:
self.progressSig.emit(self.finishedFileNum * 100 /
self.totalFileNum)
self.workflow_progress.emit(self.finishedFileNum * 100 /
self.totalFileNum)
elif info[0] == "popen":
self.list_pids.append(info[1])
elif info[0] == "error":
self.on_pushButton_2_clicked(quiet=True) #杀掉进程
self.HmmCleaner_exception.emit(
"Error happened! Click <span style='font-weight:600; color:#ff0000;'>Show log</span> to see detail!"
)
self.error_has_shown = True
elif info[0] == "popen finished":
if info[1] in self.list_pids:
self.list_pids.remove(info[1])
def popup_HmmCleaner_exception(self, text):
if not self.error_has_shown:
QMessageBox.critical(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
if "Show log" in text:
self.on_pushButton_9_clicked()
def popupAliWarning(self, bool_):
if bool_:
QMessageBox.warning(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>\"Ali\" format cannot be used by the downstream programs "
"(e.g. IQ-TREE), please uncheck it if you are going to use this result for other functions.</p>"
)
def popupAutoDec(self):
popupUI = self.factory.popUpAutoDetect("HmmCleaner", self.workPath,
self)
if not popupUI:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>"
)
return
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):
'''* Alignment Mode
* Code table(if codon mode)
* strategy
* export format'''
settings = '''<p class="title">***HmmCleaner***</p>'''
c1 = self.doubleSpinBox.value()
c2 = self.doubleSpinBox_2.value()
c3 = self.doubleSpinBox_3.value()
c4 = self.doubleSpinBox_4.value()
settings += '<p>costs: \"<a href="self.HmmCleaner_exe doubleSpinBox.setFocus() doubleSpinBox.selectAll() ' \
'factory.highlightWidgets(x.doubleSpinBox)">%s</a>\" ' \
'\"<a href="self.HmmCleaner_exe doubleSpinBox_2.setFocus() doubleSpinBox_2.selectAll() ' \
'factory.highlightWidgets(x.doubleSpinBox_2)">%s</a>\" ' \
'\"<a href="self.HmmCleaner_exe doubleSpinBox_3.setFocus() doubleSpinBox_3.selectAll() ' \
'factory.highlightWidgets(x.doubleSpinBox_3)">%s</a>\" ' \
'\"<a href="self.HmmCleaner_exe doubleSpinBox_4.setFocus() doubleSpinBox_4.selectAll() ' \
'factory.highlightWidgets(x.doubleSpinBox_4)">%s</a>\"</p>' % (c1, c2, c3, c4)
verbosity = self.comboBox_5.currentText()
settings += '<p>verbosity: <a href="self.HmmCleaner_exe comboBox_5.showPopup()' \
' factory.highlightWidgets(x.comboBox_5)">%s</a></p>' % verbosity
profile = self.comboBox_3.currentText()
settings += '<p>profile: <a href="self.HmmCleaner_exe comboBox_3.showPopup()' \
' factory.highlightWidgets(x.comboBox_3)">%s</a></p>' % profile
thread = self.comboBox_6.currentText()
settings += '<p>Thread: <a href="self.HmmCleaner_exe comboBox_6.showPopup()' \
' factory.highlightWidgets(x.comboBox_6)">%s</a></p>' % thread
specificity = "Yes" if self.checkBox.isChecked() else "No"
settings += '<p>specificity: <a href="self.HmmCleaner_exe' \
' factory.highlightWidgets(x.checkBox)">%s</a></p>' % specificity
large = "Yes" if self.checkBox_2.isChecked() else "No"
settings += '<p>large: <a href="self.HmmCleaner_exe' \
' factory.highlightWidgets(x.checkBox_2)">%s</a></p>' % large
changeID = "Yes" if self.checkBox_6.isChecked() else "No"
settings += '<p>changeID: <a href="self.HmmCleaner_exe' \
' factory.highlightWidgets(x.checkBox_6)">%s</a></p>' % changeID
noX = "Yes" if self.checkBox_5.isChecked() else "No"
settings += '<p>noX: <a href="self.HmmCleaner_exe' \
' factory.highlightWidgets(x.checkBox_5)">%s</a></p>' % noX
return settings
def isFileIn(self):
return self.comboBox_4.count()
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()
class UpdateAPP(QDialog):
'''
1.先下载新的app
2.然后解压，由于github下载的，解压会自动解压到一个新的文件夹
3.从解压的文件夹把文件移动到跟文件夹，此时判断一下文件是否存在，如果存在，就重命名.old（主程序每次启动，都会判断是否有.old文件存在，
如果有就删除；这一步如果无法重命名的话，有可能会造成失败），然后再把文件移动过去（settings和plugins文件夹会跳过）
4.重新启动程序，然后删除.old文件
'''
progressSig = pyqtSignal(int) # 控制进度条
def __init__(self, parent=None):
super(UpdateAPP, self).__init__(parent)
self.factory = Factory()
self.rootPath = self.factory.thisPath
#os.path.dirname(os.path.realpath(__file__))
# self.totalSize = totalSize if totalSize else "42389760"
# self.verticalLayout = QVBoxLayout(self)
# self.setWindowTitle("Update")
# self.setAttribute(Qt.WA_TranslucentBackground)
# self.setWindowFlags(Qt.Dialog | Qt.FramelessWindowHint)
# # self.setModal(Qt.WindowModal)
# self.progressBar = PercentProgressBar(self, showSmallCircle=True)
# self.verticalLayout.addWidget(self.progressBar)
# self.label = QLabel("<span style='font-weight:600; color:white; font: 35px;'>Downloading...</span>", self)
# self.verticalLayout.addWidget(self.label)
# self.progressSig.connect(self.downloadProgress)
def exec_unzip(self):
# self.label.setText("<span style='font-weight:600; color:white; font: 35px;'>Unpacking new file</span>")
self.worker = WorkThread(self.unzipNewApp, parent=self)
self.worker.start()
self.worker.finished.connect(self.exec_restart)
def exec_restart(self):
# self.label.setText("Update successfully")
python = sys.executable
os.execl(python, python, *sys.argv)
def downloadNewAPP(self):
if platform.system().lower() == "windows":
url = "https://raw.githubusercontent.com/dongzhang0725/PhyloSuite/master/update.zip"
elif platform.system().lower() == "darwin":
url = "https://raw.githubusercontent.com/dongzhang0725/PhyloSuite_Mac/master/update.zip"
elif platform.system().lower() == "linux":
url = "https://raw.githubusercontent.com/dongzhang0725/PhyloSuite_linux/master/update.zip"
self.downloadPath = self.rootPath + os.sep + "update.zip"
###qhttp下载
dict_args = {}
dict_args["url"] = url
dict_args["downloadPath"] = self.downloadPath
# dict_args["totalSize"] = self.totalSize
dict_args["progressSig"] = self.progressSig
httpwindow = HttpWindowDownload(parent=self, **dict_args)
httpwindow.finishSig.connect(self.exec_unzip)
httpwindow.ini_args()
def unzipNewApp(self):
file_zip = zipfile.ZipFile(self.downloadPath, 'r')
namelists = file_zip.namelist()
for num, file in enumerate(namelists):
path_root = self.rootPath + os.sep + os.path.basename(file)
if os.path.exists(path_root):
##如果已经存在的文件夹就替换名字
if os.path.basename(file) not in ["settings", "plugins"]:
##SRC和插件保留
try:
##如果重命名失败，也不能移动文件，这里是可能造成更新失败的地方
os.rename(path_root, path_root + ".old")
except:
pass
try:
file_zip.extract(file, self.rootPath)
if platform.system().lower() in ["darwin", "linux"]:
os.system("chmod 755 %s" % (self.rootPath + os.sep + file))
except:
pass
self.progressSig.emit(95 + 5 * ((num + 1) / len(namelists)))
file_zip.close()
try:
os.remove(self.downloadPath)
except:
pass
class Lg_ReANNT(QDialog, Ui_tRNA_ANNT, object):
progressSig = pyqtSignal(int) # 控制进度条
startButtonStatusSig = pyqtSignal(list)
close_sig = pyqtSignal()
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
def __init__(self, unRecognisetRNA=None, gbContent=None, predict_signal=None, parent=None):
super(Lg_ReANNT, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.setupUi(self)
self.textBrowser.setText(unRecognisetRNA)
self.gbContent = gbContent
self.predict_signal = predict_signal
self.totaltRNA = unRecognisetRNA.count(">")
# 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)
# 信号和槽
self.progressSig.connect(self.normProgress)
self.close_sig.connect(self.closeWindow)
self.exception_signal.connect(self.popupException)
@pyqtSlot()
def on_pushButton_clicked(self):
text = self.textBrowser.toPlainText()
fileName = QFileDialog.getSaveFileName(
self, "Predict tRNA", "tRNAs", "fasta Format(*.fas)")
if fileName[0]:
with open(fileName[0], "w", encoding="utf-8") as f:
f.write(text)
QMessageBox.information(
self,
"Predict tRNA",
"<p style='line-height:25px; height:25px'>File saved successfully!</p>")
@pyqtSlot()
def on_pushButton_2_clicked(self):
self.arwenContents = self.textBrowser_2.toPlainText()
if self.arwenContents:
# 进度条
self.progressDialog = self.factory.myProgressDialog(
"Please Wait", "replacing...", parent=self)
self.progressDialog.show()
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.information(
self,
"Predict tRNA",
"<p style='line-height:25px; height:25px'>No ARWEN results found!</p>")
def run_command(self):
try:
# raise BaseException
self.startButtonStatusSig.emit(
[
self.pushButton_2,
None,
"start",
None,
self.qss_file,
self])
self.reANNT = ReANNT(
self.arwenContents, self.gbContent, self.totaltRNA, self.progressSig)
self.startButtonStatusSig.emit(
[self.pushButton_2, None, "simple stop", None, self.qss_file, self])
self.close_sig.emit()
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.dict_args["exportPath"],
self.qss_file,
self])
def normProgress(self, num):
oldValue = self.progressDialog.value()
done_int = int(num)
if done_int > oldValue:
self.progressDialog.setProperty("value", done_int)
QCoreApplication.processEvents()
if done_int == 100:
self.progressDialog.close()
def closeWindow(self):
self.progressDialog.close()
self.close()
self.predict_signal.emit(self.reANNT.gbContent)
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_()
class TrimAl(QDialog, Ui_trimAl, 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)
trimAl_exception = pyqtSignal(str)
workflow_progress = pyqtSignal(int)
workflow_finished = pyqtSignal(str)
# 用于输入文件后判断用
ui_closeSig = pyqtSignal(str)
# 用于flowchart自动popup combobox等操作
showSig = pyqtSignal(QDialog)
closeSig = pyqtSignal(str, str)
##弹出识别输入文件的信号
auto_popSig = pyqtSignal(QDialog)
def __init__(self,
workPath=None,
TApath=None,
autoInputs=None,
focusSig=None,
workflow=None,
parent=None):
super(TrimAl, self).__init__(parent)
self.parent = parent
self.function_name = "trimAl"
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.TApath = TApath
self.autoInputs = autoInputs
self.setupUi(self)
# 保存设置
if not workflow:
self.trimAl_settings = QSettings(
self.thisPath + '/settings/trimAl_settings.ini',
QSettings.IniFormat)
else:
self.trimAl_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.trimAl_settings.beginGroup("Workflow")
self.trimAl_settings.beginGroup("temporary")
self.trimAl_settings.beginGroup('trimAl')
# File only, no fallback to registry or or.
self.trimAl_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.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.logGuiSig.connect(self.addText2Log)
self.trimAl_exception.connect(self.popup_trimAl_exception)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) # 自动识别可用的输入
self.comboBox_4.installEventFilter(self)
self.lineEdit_2.installEventFilter(self)
self.lineEdit_3.installEventFilter(self)
self.log_gui = self.gui4Log()
# stat output file name
self.lineEdit_2.setLineEditNoChange(True)
self.lineEdit_3.setLineEditNoChange(True)
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
# 选框联动
self.checkBox_2.toggled.connect(self.switchCheckBox1)
self.checkBox_5.toggled.connect(self.switchCheckBox1)
# self.groupBox_5.toggled.connect(lambda bool_: self.groupBox_6.setChecked(not bool_))
# self.groupBox_6.toggled.connect(lambda bool_: self.groupBox_5.setChecked(not bool_))
self.checkBox_3.toggled.connect(self.switchCheckBox2)
self.checkBox_6.toggled.connect(self.switchCheckBox2)
self.checkBox_7.toggled.connect(self.switchCheckBox2)
self.checkBox_8.toggled.connect(self.switchCheckBox2)
self.checkBox_9.toggled.connect(self.judgeInput)
self.radioButton.toggled.connect(self.Un_checkBox_9)
self.comboBox_2.currentTextChanged.connect(self.judgeComboBox_2)
self.comboBox.currentTextChanged.connect(self.judgeFormats)
self.radioButton.toggled.connect(self.controlRefineText)
self.interrupt = False
# 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_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-4-1-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
"""
self.command = self.fetchCommands()
if self.command:
self.interrupt = False
self.error_has_shown = False #保证只报一次错
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
thread = thread if len(
self.dict_args["inputFiles"]) > thread else len(
self.dict_args["inputFiles"])
thread = 1 if not self.dict_args[
"inputFiles"] else thread # compare的情况
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
@pyqtSlot()
def on_pushButton_9_clicked(self):
"""
show log
"""
self.log_gui.show()
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
alignment file
"""
fileNames = QFileDialog.getOpenFileNames(self, "Input alignment file")
if fileNames[0]:
self.input(fileNames[0])
@pyqtSlot()
def on_pushButton_4_clicked(self):
"""
set file for comparison
"""
fileName = QFileDialog.getOpenFileName(
self, "Input file containing alignment path to compare")
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):
"""
matrix file
"""
fileName = QFileDialog.getOpenFileName(self, "Input matrix file")
if fileName[0]:
base = os.path.basename(fileName[0])
self.lineEdit_3.setText(base)
self.lineEdit_3.setToolTip(fileName[0])
@pyqtSlot()
def on_pushButton_2_clicked(self, quiet=False):
"""
Stop
"""
if self.isRunning():
if (not self.workflow) and (not quiet):
reply = QMessageBox.question(
self, "Confirmation",
"<p style='line-height:25px; height:25px'>trimAl is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
else:
reply = QMessageBox.Yes
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
if (not self.workflow) and (not quiet):
QMessageBox.information(
self, "trimAl",
"<p style='line-height:25px; height:25px'>Program has been terminated!</p>"
)
self.startButtonStatusSig.emit([
self.pushButton, [self.progressBar], "except",
self.dict_args["exportPath"], self.qss_file, self
])
def run_command(self):
try:
# 清空文件夹，放在这里方便统一报错
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start",
self.dict_args["exportPath"], self.qss_file, self
])
##进度条用
# self.dict_file_progress = {os.path.basename(file): 0 for file in self.dict_args["seq_files"]}
if self.radioButton.isChecked():
async_results = [
self.pool.apply_async(run,
args=(self.dict_args, self.command,
file))
for file in self.dict_args["inputFiles"]
]
self.totalFileNum = len(self.dict_args["inputFiles"])
else:
async_results = [
self.pool.apply_async(run,
args=(self.dict_args, self.command,
self.dict_args["compareFile"]))
]
self.totalFileNum = 1
self.finishedFileNum = 0 #进度条用
self.pool.close() # 关闭进程池，防止进一步操作。如果所有操作持续挂起，它们将在工作进程终止前完成
map(ApplyResult.wait, async_results)
lst_results = [r.get() for r in async_results]
# 判断比对是否成功
trimAl_results = glob.glob(self.exportPath + os.sep +
"*_trimAl.fas")
empty_files = [
os.path.basename(file) for file in trimAl_results
if os.stat(file).st_size == 0
]
has_error = False
if not trimAl_results or empty_files:
has_error = True
log = self.textEdit_log.toPlainText()
list_commands = re.findall(r"Command: (.+)\n", log)
last_cmd = list_commands[-1] if list_commands else ""
self.trimAl_exception.emit(
"trimAl execute failed, click <span style=\"color:red\">Show log</span> to see details!"
"<br>You can also copy this command to terminal to debug: %s"
% last_cmd)
if not has_error:
self.renameSequence() #修剪后序列的名字被，需要改回来
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 trimAl, please cite:\n" + self.reference +
"\n\n" + self.time_used_des)
if (not self.interrupt) and (not has_error):
self.pool = None
self.interrupt = False
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
])
self.pool = None
self.interrupt = False
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.dict_args["exportPath"], self.qss_file, self
])
self.pool = None
self.interrupt = False
def guiSave(self):
# Save geometry
self.trimAl_settings.setValue('size', self.size())
# self.trimAl_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.trimAl_settings.setValue(name, index)
elif isinstance(obj, QCheckBox):
state = obj.isChecked()
self.trimAl_settings.setValue(name, state)
elif isinstance(obj, QRadioButton):
state = obj.isChecked()
self.trimAl_settings.setValue(name, state)
elif isinstance(obj, QDoubleSpinBox):
float_ = obj.value()
self.trimAl_settings.setValue(name, float_)
elif isinstance(obj, QLineEdit):
value = obj.text()
self.trimAl_settings.setValue(name, value)
elif isinstance(obj, QTabWidget):
index = obj.currentIndex()
self.trimAl_settings.setValue(name, index)
def guiRestore(self):
# Restore geometry
self.resize(self.trimAl_settings.value('size', QSize(732, 595)))
self.factory.centerWindow(self)
# self.move(self.trimAl_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 = [str(i + 1) for i in range(cpu_num)]
index = self.trimAl_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))
elif name == "comboBox_4":
self.input(self.autoInputs)
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
index = self.trimAl_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))
item.setToolTip(i)
model.appendRow(item)
obj.setCurrentIndex(int(index))
elif isinstance(obj, QCheckBox):
value = self.trimAl_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
elif isinstance(obj, QRadioButton):
value = self.trimAl_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
elif isinstance(obj, QDoubleSpinBox):
ini_float_ = obj.value()
float_ = self.trimAl_settings.value(name, ini_float_)
obj.setValue(float(float_))
elif isinstance(obj, QLineEdit):
if name not in ["lineEdit_3", "lineEdit_2"]:
value = self.trimAl_settings.value(
name, "") # get stored value from registry
if value:
obj.setText(value) # restore checkbox
elif isinstance(obj, QTabWidget):
index = self.trimAl_settings.value(name, 0)
obj.setCurrentIndex(int(index))
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("trimAl", 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("trimAl")
# 自动跑的时候不杀掉程序
return
if self.isRunning():
reply = QMessageBox.question(
self, "trimAl",
"<p style='line-height:25px; height:25px'>trimAl is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
else:
event.ignore()
def showEvent(self, event):
QTimer.singleShot(100, lambda: self.showSig.emit(self))
def eventFilter(self, obj, event):
# modifiers = QApplication.keyboardModifiers()
name = obj.objectName()
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()]
self.input(files)
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_2":
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(TrimAl, 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 trimAl:")
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_TrimAl_.log",
"a") as f:
f.write(text + "\n")
def save_log_to_file(self):
content = self.textEdit_log.toPlainText()
fileName = QFileDialog.getSaveFileName(self, "trimAl", "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 input(self, list_items=None):
if list_items:
self.comboBox_4.refreshInputs(list_items)
else:
self.comboBox_4.refreshInputs([])
def showCMD(self):
"""
show command
"""
self.command = self.fetchCommands()
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)
self.textEdit_cmd.textChanged.connect(self.judgeCmdText)
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 clear_lineEdit(self):
sender = self.sender()
lineEdit = sender.parent()
lineEdit.setText("")
lineEdit.setToolTip("")
def fetchCommands(self):
if (self.radioButton.isChecked() and self.comboBox_4.count()) or \
(self.radioButton_2.isChecked() and self.lineEdit_2.toolTip()):
self.interrupt = False
self.error_has_shown = False
self.dict_args = {}
self.dict_args["workPath"] = self.workPath
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + \
os.sep + "trimAl_results" + os.sep + self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
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
if self.tabWidget.tabText(
self.tabWidget.currentIndex()) == "Automated Trimming":
# 自动模式
method = self.getAutoMethod()
self.dict_args["autoMethod"] = " -%s" % method
self.dict_args["cons"] = ""
self.dict_args["gt"] = ""
self.dict_args["st"] = ""
self.dict_args["ct"] = ""
self.dict_args["w"] = ""
self.dict_args["gw"] = ""
self.dict_args["sw"] = ""
self.dict_args["cw"] = ""
else:
# 人工模式
self.dict_args["autoMethod"] = ""
self.dict_args[
"cons"] = " -cons %.1f" % self.doubleSpinBox.value()
self.dict_args[
"gt"] = " -gt %.1f" % self.doubleSpinBox_2.value()
self.dict_args[
"st"] = " -st %.1f" % self.doubleSpinBox_3.value()
self.dict_args[
"ct"] = " -ct %.1f" % self.doubleSpinBox_4.value(
) if self.checkBox_9.isChecked() else ""
self.dict_args["w"] = " -w %.1f" % self.doubleSpinBox_7.value(
) if self.checkBox_3.isChecked() else ""
self.dict_args[
"gw"] = " -gw %.1f" % self.doubleSpinBox_6.value(
) if self.checkBox_6.isChecked() else ""
self.dict_args[
"sw"] = " -sw %.1f" % self.doubleSpinBox_5.value(
) if self.checkBox_7.isChecked() else ""
self.dict_args[
"cw"] = " -cw %.1f" % self.doubleSpinBox_8.value(
) if self.checkBox_8.isChecked() else ""
self.dict_args[
"complementary"] = " -complementary" if self.checkBox.isChecked(
) else ""
self.dict_args[
"colnumbering"] = " -colnumbering" if self.checkBox_2.isChecked(
) else ""
html_file_name = self.lineEdit_4.text() if self.lineEdit_4.text(
) else "summary.html"
self.dict_args["htmlout"] = " -htmlout \"%s\"" % (
self.dict_args["exportPath"] + os.sep + "$fileBase$_" +
html_file_name) if self.checkBox_4.isChecked() else ""
self.dict_args["stat"] = " -%s" % self.comboBox_2.currentText(
).split(":")[0] if self.checkBox_5.isChecked() else ""
self.dict_args["outFormat"] = " -%s" % self.comboBox.currentText()
# 输出文件后缀
dict_suffix = {
"fasta": ".fas",
"phylip": ".phy",
"phylip3.2": ".phy",
"nexus": ".nex",
"mega": ".meg",
"clustal": ".clw",
"nbrf": ".nbrf"
}
self.dict_args["suffix"] = dict_suffix[self.comboBox.currentText()]
self.dict_args["trimAl"] = self.TApath
##输入文件
if self.radioButton.isChecked():
self.dict_args["compareFile"] = ""
self.dict_args["inputFiles"] = self.comboBox_4.fetchListsText()
command = "\"{trimAl}\" -in alignment{autoMethod}{cons}{gt}{st}{ct}" \
"{w}{gw}{sw}{cw}{complementary}{colnumbering}{htmlout}" \
"{outFormat} -out outputFile{stat}".format(**self.dict_args)
else:
# compare
self.dict_args["inputFiles"] = []
self.dict_args["compareFile"] = self.lineEdit_2.toolTip()
command = "\"{trimAl}\" -compareset setFile{autoMethod}{cons}{gt}{st}{ct}" \
"{w}{gw}{sw}{cw}{complementary}{colnumbering}{htmlout}{outFormat}" \
" -out outputFile{stat}".format(**self.dict_args)
self.reference = "Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated" \
" alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25: 1972-1973. " \
"doi: 10.1093/bioinformatics/btp348."
cmd_used = "{autoMethod}{cons}{gt}{st}{ct}{w}{gw}{sw}{cw}".format(
**self.dict_args).strip()
self.description = "Gap sites were removed with trimAl (Capella‐Gutiérrez et al., 2009) using \"%s\" command." % cmd_used
self.textEdit_log.clear() # 清空
return command
else:
if self.radioButton.isChecked():
QMessageBox.critical(
self, "trimAl",
"<p style='line-height:25px; height:25px'>Please input files to \"Input\" box first!</p>"
)
else:
QMessageBox.critical(
self, "trimAl",
"<p style='line-height:25px; height:25px'>Please input files to \"Compare set\" box first!</p>"
)
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, "pool") and self.pool and not self.interrupt
def run_with_CMD(self, cmd):
self.command = cmd
if self.command:
self.interrupt = False
self.error_has_shown = False
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
thread = thread if len(
self.dict_args["inputFiles"]) > thread else len(
self.dict_args["inputFiles"])
thread = 1 if not self.dict_args[
"inputFiles"] else thread # compare的情况
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# # Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
def judgeCmdText(self):
text = self.textEdit_cmd.toPlainText()
if self.radioButton.isChecked():
if " -in alignment" not in text:
QMessageBox.information(
self, "trimAl",
"<p style='line-height:25px; height:25px'>\"-in alignment\" cannot be changed!</p>"
)
self.textEdit_cmd.undo()
else:
if " -compareset setFile" not in text:
QMessageBox.information(
self, "trimAl",
"<p style='line-height:25px; height:25px'>\"-compareset setFile\" cannot be changed!</p>"
)
self.textEdit_cmd.undo()
def updateProcess(self):
if self.queue.empty(): return
info = self.queue.get()
if info[0] == "log":
message = info[1]
self.logGuiSig.emit(message)
elif info[0] == "prog":
self.finishedFileNum += 1
if not self.interrupt:
self.workflow_progress.emit(self.finishedFileNum * 95 /
self.totalFileNum)
self.progressSig.emit(self.finishedFileNum * 95 /
self.totalFileNum)
elif info[0] == "popen":
self.list_pids.append(info[1])
elif info[0] == "error":
self.on_pushButton_2_clicked(quiet=True) #杀掉进程
self.trimAl_exception.emit(
"Error happened! Click <span style='font-weight:600; color:#ff0000;'>Show log</span> to see detail!"
)
self.error_has_shown = True
elif info[0] == "popen finished":
if info[1] in self.list_pids:
self.list_pids.remove(info[1])
def popup_trimAl_exception(self, text):
if not self.error_has_shown:
QMessageBox.critical(
self, "trimAl",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
if "Show log" in text:
self.on_pushButton_9_clicked()
def judgeComboBox_2(self, text):
if text in ["sfc: Print compare values for columns in the selected alignment from compare files method.",
"sft: Print accumulated compare values count for the selected alignment from compare files method."] \
and self.radioButton.isChecked():
QMessageBox.information(
self, "trimAl",
"<p style='line-height:25px; height:25px'>This option should be used in combination with \"Compare set\".</p>"
)
self.comboBox_2.setCurrentIndex(0)
def switchCheckBox1(self, bool_):
checkbox = self.sender()
if (checkbox
== self.checkBox_2) and bool_ and self.checkBox_5.isChecked():
self.checkBox_5.setChecked(False)
if (checkbox
== self.checkBox_5) and bool_ and self.checkBox_2.isChecked():
self.checkBox_2.setChecked(False)
def switchCheckBox2(self, bool_):
checkbox = self.sender()
if checkbox == self.checkBox_3:
if bool_:
for i in [self.checkBox_6, self.checkBox_7, self.checkBox_8]:
i.setChecked(not bool_)
else:
if bool_:
self.checkBox_3.setChecked(not bool_)
def judgeInput(self, bool_):
if bool_ and (not self.radioButton_2.isChecked()):
QMessageBox.information(
self, "trimAl",
"<p style='line-height:25px; height:25px'>This option should be used in combination with \"Compare set\".</p>"
)
self.checkBox_9.setChecked(False)
def Un_checkBox_9(self, bool_):
if bool_:
self.checkBox_9.setChecked(not bool_)
def popupAutoDec(self, init=False):
self.init = init
self.factory.popUpAutoDetect("trimAl", 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 judgeFormats(self, text):
if text != "fasta":
QMessageBox.warning(
self, "HmmCleaner",
"<p style='line-height:25px; height:25px'>\"%s\" format cannot be used by the downstream programs "
"(e.g. concatenation), please select fasta format if you are going to use "
"this result for other functions.</p>" % text)
def renameSequence(self):
trimedFiles = glob.glob(self.exportPath + os.sep + "*_trimAl.fas")
if trimedFiles:
for num, file in enumerate(trimedFiles):
with open(file, encoding="utf-8", errors="ignore") as f:
content = f.read()
with open(file, "w", encoding="utf-8") as f1:
f1.write(re.sub(r"(>.+?) \d+ bp", "\\1", content))
self.progressSig.emit(95 + (5 * (num + 1) / len(trimedFiles)))
self.workflow_progress.emit(95 +
(5 * (num + 1) / len(trimedFiles)))
def fetchWorkflowSetting(self):
'''* Alignment Mode
* Code table(if codon mode)
* strategy
* export format'''
settings = '''<p class="title">***trimAl***</p>'''
trim_strategy = self.tabWidget.tabText(self.tabWidget.currentIndex())
settings += '<p>Trimming strategy: <a href="self.trimAl_exe' \
' factory.highlightWidgets(x.tabWidget.tabBar())">%s</a></p>' % trim_strategy
if trim_strategy == "Automated Trimming":
# settings += "|--Automated Trimming--|"
strategy = self.getAutoMethod()
settings += '<p>Automated method: <a href="self.trimAl_exe ' \
'factory.highlightWidgets(x.radioButton_10,x.radioButton_11,x.radioButton_12,' \
'x.radioButton_13,x.radioButton_14,x.radioButton_15)">%s</a></p>' % strategy
else:
# settings += "|--Manual Trimming--|"
cons = self.doubleSpinBox.value()
settings += '<p>Minimum percentage of positions to conserve [0-100]: <a href="self.trimAl_exe ' \
'doubleSpinBox.setFocus() doubleSpinBox.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox)">%s</a></p>' % cons
gaps = self.doubleSpinBox_2.value()
settings += '<p>Gap threshold, fraction of positions without gaps in a column [0-1]: <a href="self.trimAl_exe ' \
'doubleSpinBox_2.setFocus() doubleSpinBox_2.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_2)">%s</a></p>' % gaps
ss = self.doubleSpinBox_3.value()
settings += '<p>Similarity threshold, minimum level of residue similarity within a column [0-1]: <a href="self.trimAl_exe ' \
'doubleSpinBox_3.setFocus() doubleSpinBox_3.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_3)">%s</a></p>' % ss
if self.checkBox_3.isChecked():
w = self.doubleSpinBox_7.value()
settings += '<p>General window size, applied to all stats: <a href="self.trimAl_exe ' \
'doubleSpinBox_7.setFocus() doubleSpinBox_7.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_7)">%s</a></p>' % w
if self.checkBox_6.isChecked():
gw = self.doubleSpinBox_6.value()
settings += '<p>Window size applied to Gaps: <a href="self.trimAl_exe ' \
'doubleSpinBox_6.setFocus() doubleSpinBox_6.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_6)">%s</a></p>' % gw
if self.checkBox_7.isChecked():
sw = self.doubleSpinBox_5.value()
settings += '<p>Window size applied to Similarity: <a href="self.trimAl_exe ' \
'doubleSpinBox_5.setFocus() doubleSpinBox_5.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_5)">%s</a></p>' % sw
if self.checkBox_8.isChecked():
cw = self.doubleSpinBox_8.value()
settings += '<p>Window size applied to Consistency: <a href="self.trimAl_exe ' \
'doubleSpinBox_8.setFocus() doubleSpinBox_8.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_8)">%s</a></p>' % cw
thread = self.comboBox_6.currentText()
settings += '<p>Thread: <a href="self.trimAl_exe comboBox_6.showPopup()' \
' factory.highlightWidgets(x.comboBox_6)">%s</a></p>' % thread
return settings
def isFileIn(self):
return self.comboBox_4.count()
def controlRefineText(self, bool_):
if bool_:
if not self.comboBox_4.count():
self.comboBox_4.lineEdit().switchColor(
"No input files (Try to drag your file(s) and drop here)")
else:
self.comboBox_4.lineEdit().switchColor()
else:
self.comboBox_4.lineEdit().switchColor()
def getAutoMethod(self):
widgets = (self.gridLayout_8.itemAt(i).widget()
for i in range(self.gridLayout_8.count()))
checkedBox = [
widget for widget in widgets
if isinstance(widget, QRadioButton) and widget.isChecked()
][0]
return checkedBox.text()
class Matrix(QDialog, Ui_Matrix, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
# warning_signal = pyqtSignal(dict)
progressSig = pyqtSignal(int) # 控制进度条
startButtonStatusSig = pyqtSignal(list)
unalignedSig = pyqtSignal(list)
workflow_progress = pyqtSignal(int)
workflow_finished = pyqtSignal(str)
##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)
def __init__(self,
files=None,
workPath=None,
focusSig=None,
workflow=False,
parent=None):
super(Matrix, self).__init__(parent)
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
# 保存设置
if not workflow:
self.concatenate_settings = QSettings(
self.thisPath + '/settings/concatenate_settings.ini',
QSettings.IniFormat)
else:
self.concatenate_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.concatenate_settings.beginGroup("Workflow")
self.concatenate_settings.beginGroup("temporary")
self.concatenate_settings.beginGroup('Concatenate Sequence')
# File only, no fallback to registry or or.
self.concatenate_settings.setFallbacksEnabled(False)
self.setupUi(self)
self.files = files
self.workPath = workPath
self.focusSig = focusSig if focusSig else pyqtSignal(
str) # 为了方便workflow
self.workflow = workflow
# 恢复用户的设置
self.guiRestore()
# 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)
self.groupBox_top_line.setStyleSheet('''QGroupBox{
border-bottom:none;
border-right:none;
border-left:none;
}
QGroupBox::title{
subcontrol-origin: margin;
subcontrol-position: top left;
}''')
self.unalignedSig.connect(self.unaligned)
self.exception_signal.connect(self.popupException)
# self.warning_signal.connect(self.popupWarning)
self.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
self.progressSig.connect(self.runProgress)
self.comboBox_4.installEventFilter(self)
self.comboBox_4.lineEdit().autoDetectSig.connect(
self.popupAutoDec) #自动识别可用的输入
##设置拖拽排序
self.comboBox_4.view().setDragEnabled(True)
self.comboBox_4.view().setDragDropMode(QAbstractItemView.InternalMove)
self.comboBox_4.view().setDefaultDropAction(Qt.MoveAction)
# self.comboBox_4.view().setSelectionMode(QAbstractItemView.MultiSelection)
self.comboBox_4.view().installEventFilter(self)
# 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_2.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-7-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
if self.isFileIn():
self.dict_args = {}
self.dict_args["parent"] = self
self.dict_args["exception_signal"] = self.exception_signal
# self.dict_args["warning_signal"] = self.warning_signal
self.dict_args["unaligned_signal"] = self.unalignedSig
self.dict_args["progressSig"] = self.progressSig
self.dict_args["workflow_progress"] = self.workflow_progress
self.dict_args["files"] = self.comboBox_4.fetchListsText()
self.dict_args["workPath"] = self.workPath
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + os.sep +
"concatenate_results" +
os.sep +
self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
self.dict_args["export_phylip"] = self.checkBox.isChecked()
self.dict_args["export_nex"] = self.checkBox_2.isChecked()
self.dict_args["export_nexi"] = self.checkBox_3.isChecked()
self.dict_args["export_nexig"] = self.checkBox_4.isChecked()
self.dict_args["export_axt"] = self.checkBox_13.isChecked()
self.dict_args["export_paml"] = self.checkBox_5.isChecked()
self.dict_args["export_fas"] = self.checkBox_12.isChecked()
self.dict_args["export_stat"] = self.checkBox_9.isChecked()
self.dict_args["export_name"] = self.lineEdit.text(
) if self.lineEdit.text() else "concatenation"
if self.groupBox_top_line.isChecked():
self.dict_args["draw_linear"] = True
self.dict_args["fig_height"] = self.spinBox_5.value()
self.dict_args["fig_width"] = self.spinBox_6.value()
self.dict_args["label_size"] = self.spinBox_7.value()
self.dict_args["Label_angle"] = self.spinBox_8.value()
self.dict_args["Label_position"] = self.comboBox.currentText()
self.dict_args["Label_color"] = self.pushButton_color.text()
else:
self.dict_args["draw_linear"] = False
if True not in list(self.dict_args.values()):
QMessageBox.critical(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>Please select output format(s) first!</p>"
)
self.checkBox.setChecked(True)
return
##描述，方便worfflow使用
self.description = ""
self.reference = ""
ok = self.factory.remove_dir(self.dict_args["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
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
else:
QMessageBox.critical(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>Please input files first!</p>"
)
def run_command(self):
try:
# 先清空文件夹
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start",
self.dict_args["exportPath"], self.qss_file, self
])
self.seqMatrix = Seq_matrix(**self.dict_args)
if not self.seqMatrix.ok:
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.dict_args["exportPath"], self.qss_file, self
])
return
if "draw_linear" in self.dict_args and self.dict_args[
"draw_linear"]:
self.dict_args[
"partition_file"] = self.seqMatrix.partition_detail
Partition2fig(**self.dict_args)
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.dict_args["exportPath"] + os.sep + "summary.txt",
"w",
encoding="utf-8") as f:
f.write(
"If you use PhyloSuite, please cite:\nZhang, D., Gao, F., Li, W.X., Jakovlić, I., Zou, H., Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. bioRxiv, doi: 10.1101/489088.\n\n"
+ self.time_used_des)
if not self.seqMatrix.unaligned and not self.seqMatrix.interrupt:
if self.workflow:
##work flow跑的
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "workflow stop",
self.dict_args["exportPath"], self.qss_file, self
])
self.workflow_finished.emit("finished")
return
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "stop",
self.dict_args["exportPath"], self.qss_file, self
])
else:
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.dict_args["exportPath"], self.qss_file, self
])
if not self.workflow:
self.focusSig.emit(self.dict_args["exportPath"])
self.seqMatrix.interrupt = True
# self.seqMatrix.supplement()
# if self.seqMatrix.dist_warning_message:
# self.dict_args["warning_signal"].emit(
# self.seqMatrix.dist_warning_message)
# else:
# # if self.mafft_interrupt is not True:
# self.seqMatrix.concatenate()
# if not self.seqMatrix.unaligned and not self.seqMatrix.interrupt:
# if self.workflow:
# ##work flow跑的
# self.startButtonStatusSig.emit(
# [
# self.pushButton,
# self.progressBar,
# "workflow stop",
# self.dict_args["exportPath"],
# self.qss_file,
# self])
# self.workflow_finished.emit("finished")
# return
# self.startButtonStatusSig.emit(
# [self.pushButton, self.progressBar, "stop", self.dict_args["exportPath"], self.qss_file, self])
# else:
# self.startButtonStatusSig.emit(
# [self.pushButton, self.progressBar, "except", self.dict_args["exportPath"], self.qss_file,
# self])
# if not self.workflow:
# self.focusSig.emit(self.dict_args["exportPath"])
# self.seqMatrix.interrupt = True
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.dict_args["exportPath"], self.qss_file, self
])
@pyqtSlot()
def on_pushButton_2_clicked(self):
"""
Stop
"""
if self.isRunning():
self.seqMatrix.interrupt = True
if not self.workflow:
QMessageBox.information(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>Concatenation has been terminated!</p>"
)
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "except",
self.dict_args["exportPath"], self.qss_file, self
])
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
open files
"""
files = QFileDialog.getOpenFileNames(
self,
"Input Files",
filter=
"Supported Format(*.fas *.fasta *.phy *.phylip *.nex *.nxs *.nexus);;"
)
if files[0]:
self.input(files[0])
def unaligned(self, message):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(
"<p style='line-height:25px; height:25px'>Unaligned sequences found, see details</p>"
)
msg.setWindowTitle("Error")
msg.setDetailedText("Unaligned sequences: " + ",".join(message))
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
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):
rgx = re.compile(r'Permission.+?[\'\"](.+\.csv)[\'\"]')
if rgx.search(exception):
csvfile = rgx.search(exception).group(1)
reply = QMessageBox.critical(
self, "Concatenate 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_()
@pyqtSlot(OrderedDict)
def popupWarning(self, dist_warning):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Information)
msg.setText(
"<p style='line-height:25px; height:25px'>Missing genes are replaced with '?' (see details or 'missing_genes.txt')</p>"
)
msg.setWindowTitle("Concatenation Warning")
max_len_taxa = len(max(list(dist_warning), key=len))
max_len_taxa = max_len_taxa if max_len_taxa > 7 else 7 #要大于species的占位符
list_detail = ["Species".ljust(max_len_taxa) + " |Missing genes"] + [
str(i).ljust(max_len_taxa) + " |" + str(dist_warning[i])
for i in dist_warning
]
# html_detail = "<html>" + "\n".join(list_detail).replace(" ", " ") + "</html>"
msg.setDetailedText("\n".join(list_detail))
msg.setStandardButtons(QMessageBox.Ok)
with open(self.dict_args["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:
# self.seqMatrix.concatenate()
# if self.workflow:
# ##work flow跑的
# self.startButtonStatusSig.emit(
# [
# self.pushButton,
# self.progressBar,
# "workflow stop",
# self.dict_args["exportPath"],
# self.qss_file,
# self])
# self.workflow_finished.emit("finished")
# return
# self.startButtonStatusSig.emit(
# [self.pushButton, self.progressBar, "stop", self.dict_args["exportPath"], self.qss_file, self])
# self.focusSig.emit(self.dict_args["exportPath"])
# self.seqMatrix.interrupt = True
def guiSave(self):
# Save geometry
self.concatenate_settings.setValue('size', self.size())
# self.concatenate_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, QCheckBox):
state = obj.isChecked()
self.concatenate_settings.setValue(name, state)
if isinstance(obj, QLineEdit):
text = obj.text()
self.concatenate_settings.setValue(name, text)
if isinstance(obj, QSpinBox):
value = obj.value()
self.concatenate_settings.setValue(name, value)
if isinstance(obj, QPushButton):
if name == "pushButton_color":
color = obj.palette().color(1)
self.concatenate_settings.setValue(name, color.name())
if isinstance(obj, QComboBox):
if name == "comboBox":
# save combobox selection to registry
index = obj.currentIndex()
self.concatenate_settings.setValue(name, index)
if isinstance(obj, QGroupBox):
state = obj.isChecked()
self.concatenate_settings.setValue(name, state)
def guiRestore(self):
# Restore geometry
self.resize(self.concatenate_settings.value('size', QSize(500, 500)))
# self.move(self.concatenate_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox":
allItems = [obj.itemText(i) for i in range(obj.count())]
index = self.concatenate_settings.value(name, "0")
if type(index) != str:
index = "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))
else:
if self.files:
self.input(self.files)
else:
self.input([])
if isinstance(obj, QCheckBox):
value = self.concatenate_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QLineEdit):
text = self.concatenate_settings.value(name, "concatenation")
obj.setText(text)
if isinstance(obj, QSpinBox):
value = self.concatenate_settings.value(name, None)
if value:
obj.setValue(int(value))
if isinstance(obj, QGroupBox):
value = self.concatenate_settings.value(
name, "true") # get stored value from registry
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
if isinstance(obj, QPushButton):
if name == "pushButton_color":
color = self.concatenate_settings.value(name, "#F9C997")
obj.setStyleSheet("background-color:%s" % color)
obj.setText(color)
obj.clicked.connect(self.changePbColor)
def closeEvent(self, event):
self.guiSave()
self.closeSig.emit("Concatenation", self.fetchWorkflowSetting())
self.lineEdit.clearFocus()
self.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("Concatenation")
## 自动跑的时候不杀掉程序
return
if self.isRunning():
# print(self.isRunning())
reply = QMessageBox.question(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>Concatenation is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
self.seqMatrix.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()]
files = [
i for i in files if os.path.splitext(i)[1].upper() in [
".FAS", ".FASTA", ".PHY", ".PHYLIP", ".NEX", ".NXS",
".NEXUS"
]
]
self.input(files)
if isinstance(obj, QListWidget):
if event.type() == QEvent.ChildRemoved:
obj.setDragEnabled(True)
obj.setDragDropMode(QAbstractItemView.InternalMove)
obj.setDefaultDropAction(Qt.MoveAction)
list_inputs = self.comboBox_4.fetchListsText()
self.comboBox_4.refreshInputs(list_inputs, sort=False)
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(Matrix, self).eventFilter(obj, event) # 0
def input(self, files):
empty_files = []
rest_files = []
for file in files:
if os.stat(file).st_size == 0:
empty_files.append(os.path.basename(file))
else:
rest_files.append(file)
if empty_files:
if len(empty_files) > 1:
word1 = "files are"
word2 = "they will"
else:
word1 = "file is"
word2 = "it will"
QMessageBox.warning(
self, "Concatenation",
"<p style='line-height:25px; height:25px'>%s %s empty, %s be ignored!</p>"
% (str(empty_files), word1, word2), QMessageBox.Ok)
self.comboBox_4.refreshInputs(rest_files)
def isRunning(self):
if hasattr(self, "seqMatrix") and (not self.seqMatrix.interrupt):
return True
else:
return False
def popupAutoDec(self):
popupUI = self.factory.popUpAutoDetect("Concatenation", self.workPath,
self)
if not popupUI:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>"
)
return
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):
'''
export format;
export name
'''
settings = '''<p class="title">***Concatenate Sequence***</p>'''
list_formats = []
for checkbox in [
self.checkBox, self.checkBox_2, self.checkBox_3,
self.checkBox_4, self.checkBox_5, self.checkBox_9,
self.checkBox_12, self.checkBox_13
]:
if checkbox.isChecked():
list_formats.append(checkbox.text())
formats = ", ".join(list_formats) if list_formats else "None"
settings += '<p>Export formats: <a href="self.Concatenation_exe ' \
'factory.highlightWidgets(x.checkBox,x.checkBox_2,x.checkBox_3,x.checkBox_4,x.checkBox_5,' \
'x.checkBox_9,x.checkBox_12,x.checkBox_13)">%s</a></p>'%formats
export_name = self.lineEdit.text()
settings += '<p>Export file name: <a href="self.Concatenation_exe lineEdit.setFocus()' \
' lineEdit.selectAll() factory.highlightWidgets(x.lineEdit)">%s</a></p>'%export_name
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()
def changePbColor(self):
button = self.sender()
ini_color = button.palette().color(1)
color = QColorDialog.getColor(QColor(ini_color), self)
if color.isValid():
button.setText(color.name())
button.setStyleSheet("background-color:%s" % color.name())
@pyqtSlot(str)
def popupEmptyFileWarning(self, text):
QMessageBox.warning(
self, "Concatenation Warning",
"<p style='line-height:25px; height:25px'>%s!</p>" % text)
class MACSE(QDialog, Ui_MACSE, 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)
# 用于输入文件后判断用
ui_closeSig = pyqtSignal(str)
# 用于flowchart自动popup combobox等操作
showSig = pyqtSignal(QDialog)
closeSig = pyqtSignal(str, str)
# 比对完有空文件报错
emptySig = pyqtSignal(str)
def __init__(self,
workPath=None,
focusSig=None,
workflow=False,
java=None,
macseEXE=None,
autoMFPath=None,
parent=None):
super(MACSE, self).__init__(parent)
self.parent = parent
self.workflow = workflow
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.focusSig = focusSig
self.java = java
self.macseEXE = macseEXE
self.autoMFPath = autoMFPath
self.setupUi(self)
# 保存设置
if not workflow:
self.MACSE_settings = QSettings(
self.thisPath + '/settings/MACSE_settings.ini',
QSettings.IniFormat)
else:
self.MACSE_settings = QSettings(
self.thisPath + '/settings/workflow_settings.ini',
QSettings.IniFormat)
self.MACSE_settings.beginGroup("Workflow")
self.MACSE_settings.beginGroup("temporary")
self.MACSE_settings.beginGroup('MACSE')
# File only, no fallback to registry or or.
self.MACSE_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.startButtonStatusSig.connect(self.factory.ctrl_startButton_status)
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_5.installEventFilter(self)
self.comboBox_7.installEventFilter(self)
self.log_gui = self.gui4Log()
# self.pushButton_2.clicked.connect(print)
self.doubleSpinBox_5.valueChanged.connect(self.judgeStopCost)
self.doubleSpinBox.valueChanged.connect(self.judgeStopCost)
self.doubleSpinBox_2.valueChanged.connect(self.judgeStoplrCost)
self.doubleSpinBox_6.valueChanged.connect(self.judgeStoplrCost)
self.comboBox_5.itemRemovedSig.connect(self.judgeCombobox5)
self.checkBox_2.toggled.connect(self.controlRefineText)
self.emptySig.connect(self.popup_MACSE_exception)
self.interrupt = False
# 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_7.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-3-1-Brief-example"
)))
@pyqtSlot()
def on_pushButton_clicked(self):
"""
execute program
"""
self.command = self.fetchCommands()
if self.command:
self.interrupt = False
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
if self.dict_args["refine"]:
thread = thread if len(
self.dict_args["alignment"]) > thread else len(
self.dict_args["alignment"])
else:
thread = thread if len(
self.dict_args["seq_files"]) > thread else len(
self.dict_args["seq_files"])
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
@pyqtSlot()
def on_pushButton_3_clicked(self):
"""
sequence file
"""
fileNames = QFileDialog.getOpenFileNames(
self,
"Input sequence file",
filter="Fasta Format(*.fas *.fasta *.fa *.fna);;")
if fileNames[0]:
self.input(self.comboBox_4, fileNames[0])
@pyqtSlot()
def on_pushButton_4_clicked(self):
"""
less reliable sequence file
"""
fileNames = QFileDialog.getOpenFileNames(
self,
"Input sequence file",
filter="Fasta Format(*.fas *.fasta *.fa *.fna);;")
if fileNames[0]:
self.input(self.comboBox_5, fileNames[0])
@pyqtSlot()
def on_pushButton_22_clicked(self):
"""
alignment
"""
fileNames = QFileDialog.getOpenFileNames(
self,
"Input alignment",
filter="Fasta Format(*.fas *.fasta *.fa *.fna);;")
if fileNames[0]:
self.input(self.comboBox_7, 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'>MACSE is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
else:
reply = QMessageBox.Yes
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
if not self.workflow:
QMessageBox.information(
self, "MACSE",
"<p style='line-height:25px; height:25px'>Program has been terminated!</p>"
)
self.startButtonStatusSig.emit([
self.pushButton, [self.progressBar], "except",
self.dict_args["exportPath"], self.qss_file, self
])
def run_command(self):
try:
# 清空文件夹，放在这里方便统一报错
time_start = datetime.datetime.now()
self.startButtonStatusSig.emit([
self.pushButton, self.progressBar, "start",
self.dict_args["exportPath"], self.qss_file, self
])
##进度条用
if self.dict_args["refine"]:
self.dict_file_progress = {
os.path.basename(file): 0
for file in self.dict_args["alignment"]
}
async_results = [
self.pool.apply_async(run,
args=(self.dict_args, self.command,
file, num))
for num, file in enumerate(self.dict_args["alignment"])
]
else:
self.dict_file_progress = {
os.path.basename(file): 0
for file in self.dict_args["seq_files"]
}
async_results = [
self.pool.apply_async(run,
args=(self.dict_args, self.command,
file, num))
for num, file in enumerate(self.dict_args["seq_files"])
]
self.pool.close() # 关闭进程池，防止进一步操作。如果所有操作持续挂起，它们将在工作进程终止前完成
map(ApplyResult.wait, async_results)
lst_results = [r.get() for r in async_results]
# 判断比对是否成功
macse_NT_results = glob.glob(self.dict_args["exportPath"] +
os.sep + "*_NT.*")
empty_files = [
os.path.basename(file) for file in macse_NT_results
if os.stat(file).st_size == 0
]
has_error = False
refine_nopt = True if (self.checkBox_2.isChecked()
and self.comboBox_2.currentText() == "NONE"
) else False #fefine模式，并且不optimization
if not macse_NT_results or empty_files:
log = self.textEdit_log.toPlainText()
list_commands = re.findall(r"Command: (.+)\n", log)
last_cmd = list_commands[-1] if list_commands else ""
if ("StringIndexOutOfBoundsException"
in log) and ("-prog refineAlignment" in log):
has_error = True
self.emptySig.emit(
"MACSE executes failed, click <span style=\"color:red\">Show log</span> to see details! "
"<br>As you selected \"Refine\", please ensure that your input files are aligned. "
"<br>You can also copy this command to terminal to debug: %s"
% last_cmd)
elif not refine_nopt:
has_error = True
# if self.checkBox_2.isChecked():
# self.emptySig.emit("MACSE executes failed, click <span style=\"color:red\">Show log</span> to see details! "
# "<br>As you selected \"Refine\", please ensure that your input files are aligned. "
# "<br>You can also copy this command to terminal to debug: %s" % last_cmd)
# else:
self.emptySig.emit(
"MACSE execute failed, click <span style=\"color:red\">Show log</span> to see details! "
"<br>You can also copy this command to terminal to debug: %s"
% last_cmd)
if not has_error:
# 替换感叹号和星号，以便下游程序调用
macse_AA_results = glob.glob(self.dict_args["exportPath"] +
os.sep + "*_AA.*")
self.replaceSymbols(macse_NT_results + macse_AA_results)
##预防optimization为0的时候
self.progressSig.emit(100)
self.workflow_progress.emit(100)
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., Gao, F., Li, W.X., Jakovlić, I., Zou, H., Zhang, J., and Wang, G.T. (2018). PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. bioRxiv, doi: 10.1101/489088.\n"
"If you use MACSE, please cite:\n" + self.reference +
"\n\n" + self.time_used_des)
if (not self.interrupt) and (not has_error):
self.pool = None
self.interrupt = False
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
])
self.pool = None
self.interrupt = False
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.dict_args["exportPath"], self.qss_file, self
])
self.pool = None
self.interrupt = False
def guiSave(self):
# Save geometry
self.MACSE_settings.setValue('size', self.size())
# self.MACSE_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.MACSE_settings.setValue(name, index)
if isinstance(obj, QCheckBox):
state = obj.isChecked()
self.MACSE_settings.setValue(name, state)
elif isinstance(obj, QSpinBox):
value = obj.value()
self.MACSE_settings.setValue(name, value)
elif isinstance(obj, QDoubleSpinBox):
float_ = obj.value()
self.MACSE_settings.setValue(name, float_)
elif isinstance(obj, QLineEdit):
value = obj.text()
self.MACSE_settings.setValue(name, value)
def guiRestore(self):
# Restore geometry
self.resize(self.MACSE_settings.value('size', QSize(679, 693)))
# self.move(self.MACSE_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 = [str(i + 1) for i in range(cpu_num)]
index = self.MACSE_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))
elif name == "comboBox_4":
if self.autoMFPath and (not "_mafft."
in self.autoMFPath[0]):
self.input(self.comboBox_4, self.autoMFPath)
self.input(self.comboBox_7, [])
else:
self.input(self.comboBox_4, [])
elif name == "comboBox_5":
self.input(self.comboBox_5, None)
elif name == "comboBox_7":
if self.autoMFPath and ("_mafft." in self.autoMFPath[0]):
## MAFFT的结果导入
self.checkBox_2.setChecked(True)
self.input(self.comboBox_7, self.autoMFPath)
self.input(self.comboBox_4, [])
else:
self.input(self.comboBox_7, [])
else:
allItems = [obj.itemText(i) for i in range(obj.count())]
index = self.MACSE_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, QCheckBox):
value = self.MACSE_settings.value(
name, "no setting") # get stored value from registry
if value != "no setting":
obj.setChecked(
self.factory.str2bool(value)) # restore checkbox
elif isinstance(obj, QSpinBox):
ini_value = obj.value()
value = self.MACSE_settings.value(name, ini_value)
obj.setValue(int(value))
elif isinstance(obj, QDoubleSpinBox):
ini_float_ = obj.value()
float_ = self.MACSE_settings.value(name, ini_float_)
obj.setValue(float(float_))
elif isinstance(obj, QLineEdit):
value = self.MACSE_settings.value(
name, "") # get stored value from registry
if value:
obj.setText(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):
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("MACSE", 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("MACSE")
# 自动跑的时候不杀掉程序
return
if self.isRunning():
reply = QMessageBox.question(
self, "MACSE",
"<p style='line-height:25px; height:25px'>MACSE is still running, terminate it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
try:
self.worker.stopWork()
self.pool.terminate(
) # Terminate all processes in the Pool
## 删除subprocess
if platform.system().lower() == "windows":
for pid in self.list_pids:
os.popen('taskkill /F /T /PID %s' % pid)
else:
for pid in self.list_pids:
os.killpg(os.getpgid(pid), signal.SIGTERM)
self.pool = None
self.interrupt = True
except:
self.pool = None
self.interrupt = True
else:
event.ignore()
def showEvent(self, event):
QTimer.singleShot(100, lambda: self.showSig.emit(self))
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()]
self.input(obj, files)
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(MACSE, 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 MACSE:")
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)
def save_log_to_file(self):
content = self.textEdit_log.toPlainText()
fileName = QFileDialog.getSaveFileName(self, "MACSE", "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 input(self, combobox, list_items=None):
if list_items:
combobox.refreshInputs(list_items)
else:
combobox.refreshInputs([])
if combobox == self.comboBox_5:
self.comboBox_5.lineEdit().setText("Optional!")
elif combobox == self.comboBox_7:
self.comboBox_7.lineEdit().setText(
"No input MSA (Improves previously computed alignments)")
def judgeStopCost(self, value):
stop_value = self.doubleSpinBox_5.value()
fs_value = self.doubleSpinBox.value()
if stop_value >= (2 * fs_value):
QMessageBox.information(
self, "MACSE",
"<p style='line-height:25px; height:25px'>The value of \"stop\" should be less than twice the value of \"fs\".</p>"
)
self.doubleSpinBox.setValue(30.0)
self.doubleSpinBox_5.setValue(50.0)
def judgeStoplrCost(self, value):
stop_value = self.doubleSpinBox_6.value()
fs_value = self.doubleSpinBox_2.value()
if stop_value >= (2 * fs_value):
QMessageBox.information(
self, "MACSE",
"<p style='line-height:25px; height:25px'>The value of \"stop_lr\" should be less than twice the value of \"fs_lr\".</p>"
)
self.doubleSpinBox_2.setValue(10.0)
self.doubleSpinBox_6.setValue(17.0)
def fetchCommands(self):
if self.isFileIn():
self.interrupt = False
self.dict_args = {}
self.dict_args[
"allowNT"] = " -allow_NT \"%s\"" % self.lineEdit.text(
) if self.lineEdit.text() else ""
self.dict_args[
"alphabetAA"] = " -alphabet_AA %s" % self.comboBox.currentText(
)
self.dict_args[
"ambiOFF"] = " -ambi_OFF true" if self.checkBox.isChecked(
) else ""
self.dict_args["fs"] = " -fs %.1f" % self.doubleSpinBox.value(
) if self.doubleSpinBox.value() != 30.0 else ""
self.dict_args[
"fs_lr"] = " -fs_lr %.1f" % self.doubleSpinBox_2.value(
) if self.doubleSpinBox_2.value() != 10.0 else ""
self.dict_args[
"fs_lr_term"] = " -fs_lr_term %.1f" % self.doubleSpinBox_3.value(
) if self.doubleSpinBox_3.value() != 7.0 else ""
self.dict_args[
"fs_term"] = " -fs_term %.1f" % self.doubleSpinBox_4.value(
) if self.doubleSpinBox_4.value() != 10.0 else ""
self.dict_args[
"gap_ext"] = " -gap_ext %.1f" % self.doubleSpinBox_7.value(
) if self.doubleSpinBox_7.value() != 1.0 else ""
self.dict_args[
"gap_ext_term"] = " -gap_ext_term %.1f" % self.doubleSpinBox_9.value(
) if self.doubleSpinBox_9.value() != 0.9 else ""
self.dict_args[
"gap_op"] = " -gap_op %.1f" % self.doubleSpinBox_8.value(
) if self.doubleSpinBox_8.value() != 7.0 else ""
self.dict_args[
"gap_op_term"] = " -gap_op_term %.1f" % self.doubleSpinBox_10.value(
) if self.doubleSpinBox_10.value() != 6.3 else ""
self.dict_args[
"local_realign_dec"] = " -local_realign_dec %.1f" % self.doubleSpinBox_11.value(
) if self.doubleSpinBox_11.value() != 0.5 else ""
self.dict_args[
"local_realign_init"] = " -local_realign_init %.1f" % self.doubleSpinBox_12.value(
) if self.doubleSpinBox_12.value() != 0.5 else ""
self.dict_args[
"max_refine_iter"] = " -max_refine_iter %d" % self.spinBox.value(
) if self.spinBox.value() != -1 else ""
self.dict_args["gc_def"] = " -gc_def %s" % str(
self.comboBox_9.currentText()).split(" ")[0]
if self.comboBox_2.currentText() == "NONE":
self.dict_args["optim"] = " -optim 0"
elif self.comboBox_2.currentText() == "BASIC":
self.dict_args["optim"] = " -optim 1"
else:
self.dict_args["optim"] = ""
self.dict_args["score_matrix"] = " -score_matrix %s" % str(
self.comboBox_3.currentText())
self.dict_args[
"stop"] = " -stop %.1f" % self.doubleSpinBox_5.value(
) if self.doubleSpinBox_5.value() != 50.0 else ""
self.dict_args[
"stop_lr"] = " -stop_lr %.1f" % self.doubleSpinBox_6.value(
) if self.doubleSpinBox_6.value() != 17.0 else ""
self.dict_args["java"] = self.java
self.dict_args["macseEXE"] = self.macseEXE
self.dict_args["refine"] = self.checkBox_2.isChecked()
self.dict_args["prog"] = "alignSequences" if not self.dict_args[
"refine"] else "refineAlignment"
self.dict_args["algn_cmd"] = " -align alignment" if self.dict_args[
"refine"] else ""
self.reference = "Ranwez V, Douzery EJP, Cambon C, Chantret N, Delsuc F. 2018. MACSE v2: Toolkit for the " \
"Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons. Mol Biol Evol. " \
"35: 2582-2584. doi: 10.1093/molbev/msy159."
prefix = "The sequences were aligned" if not self.dict_args[
"refine"] else "The alignments were refined"
self.description = "%s using the codon-aware program MACSE v. 2.03 (Ranwez et al., 2018), " \
"which preserves reading frame and allows incorporation of sequencing errors or " \
"sequences with frameshifts."%prefix
# self.dict_args["exception_signal"] = self.exception_signal
# self.dict_args["progressSig"] = self.progressSig
self.dict_args["workPath"] = self.workPath
self.output_dir_name = self.factory.fetch_output_dir_name(
self.dir_action)
self.exportPath = self.factory.creat_dirs(self.workPath + \
os.sep + "MACSE_results" + os.sep + self.output_dir_name)
self.dict_args["exportPath"] = self.exportPath
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
##拷贝输入文件进去
self.dict_args["seq_files"] = []
self.dict_args["seq_lr_files"] = []
self.dict_args["alignment"] = []
try:
for seq_file in self.comboBox_4.fetchListsText():
self.dict_args["seq_files"].append(
shutil.copy(seq_file, self.exportPath))
for seq_lr_file in self.comboBox_5.fetchListsText():
self.dict_args["seq_lr_files"].append(
shutil.copy(seq_lr_file, self.exportPath))
for alin in self.comboBox_7.fetchListsText():
self.dict_args["alignment"].append(
shutil.copy(alin, self.exportPath))
except:
QMessageBox.information(
self, "MACSE",
"<p style='line-height:25px; height:25px'>File copying failed, please check your input files!</p>"
)
return
command = "\"{java}\" -jar \"{macseEXE}\" -prog {prog}{allowNT}{alphabetAA}{ambiOFF}{fs}{fs_lr}" \
"{fs_lr_term}{fs_term}{gap_ext}{gap_ext_term}{gap_op}{gap_op_term}{local_realign_dec}" \
"{local_realign_init}{max_refine_iter}{gc_def}{optim}{score_matrix}{stop}{stop_lr}" \
"{algn_cmd} -seq seqFile -seq_lr seqLrFile".format(**self.dict_args)
self.textEdit_log.clear() # 清空
return command
else:
if self.checkBox_2.isChecked():
QMessageBox.critical(
self, "MACSE",
"<p style='line-height:25px; height:25px'>Please input files to \"Refine\" box first!</p>"
)
else:
QMessageBox.critical(
self, "MACSE",
"<p style='line-height:25px; height:25px'>Please input files to \"Seq.\" box first!</p>"
)
@pyqtSlot(str, result=bool)
def fetchPopen(self, command):
self.MS_popen = self.factory.init_popen(command)
return True
def showCMD(self):
"""
show command
"""
self.command = self.fetchCommands()
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)
self.textEdit_cmd.textChanged.connect(self.judgeCmdText)
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 judgeCombobox5(self):
if not self.comboBox_5.fetchListsText():
self.comboBox_5.lineEdit().setText("Optional!")
def run_with_CMD(self, cmd):
self.command = cmd
if self.command:
self.interrupt = False
self.list_pids = []
self.queue = multiprocessing.Queue()
thread = int(self.comboBox_6.currentText())
thread = thread if len(
self.dict_args["seq_files"]) > thread else len(
self.dict_args["seq_files"])
self.pool = multiprocessing.Pool(processes=thread,
initializer=pool_init,
initargs=(self.queue, ))
# Check for progress periodically
self.timer = QTimer()
self.timer.timeout.connect(self.updateProcess)
self.timer.start(1)
self.worker = WorkThread(self.run_command, parent=self)
self.worker.start()
def judgeCmdText(self):
text = self.textEdit_cmd.toPlainText()
judge_text = "%s -seq seqFile -seq_lr seqLrFile" % self.dict_args[
"algn_cmd"]
if judge_text not in text:
QMessageBox.information(
self, "MACSE",
"<p style='line-height:25px; height:25px'>\"%s\" cannot be changed!</p>"
% judge_text)
self.textEdit_cmd.undo()
def updateProcess(self):
if self.queue.empty(): return
info = self.queue.get()
if info[0] == "log":
message = info[1]
self.logGuiSig.emit(message)
elif info[0] == "prog":
flag, file, progress = info
self.dict_file_progress[file] = progress
total_progress = 0.95 * (sum(self.dict_file_progress.values()) /
len(self.dict_file_progress))
self.workflow_progress.emit(total_progress)
self.progressSig.emit(total_progress)
elif info[0] == "popen":
self.list_pids.append(info[1])
elif info[0] == "popen finished":
if info[1] in self.list_pids:
self.list_pids.remove(info[1])
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, "pool") and self.pool and not self.interrupt
def popupAutoDec(self):
popupUI = self.factory.popUpAutoDetect("MACSE", self.workPath, self)
if not popupUI:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>No available file detected!</p>"
)
return
popupUI.checkBox.setVisible(False)
if popupUI.exec_() == QDialog.Accepted:
widget = popupUI.listWidget_framless.itemWidget(
popupUI.listWidget_framless.selectedItems()[0])
autoInputs = widget.autoInputs
self.input(self.comboBox_4, autoInputs)
def fetchWorkflowSetting(self):
'''* Alignment Mode
* Code table(if codon mode)
* strategy
* export format'''
settings = '''<p class="title">***MACSE (Aligns nucleotide coding sequences)***</p>''' if not \
self.checkBox_2.isChecked() else '''<p class="title">***MACSE (Improves a previously computed alignment)***</p>'''
code_table = self.comboBox_9.currentText()
settings += '<p>Code table: <a href="self.MACSE_exe comboBox_9.showPopup()' \
' factory.highlightWidgets(x.comboBox_9)">%s</a></p>' % code_table
Alphabet_AA = self.comboBox.currentText()
settings += '<p>Alphabet_AA: <a href="self.MACSE_exe comboBox.showPopup()' \
' factory.highlightWidgets(x.comboBox)">%s</a></p>' % Alphabet_AA
fs = self.doubleSpinBox.value()
settings += '<p>fs: <a href="self.MACSE_exe doubleSpinBox.setFocus() doubleSpinBox.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox)">%s</a></p>' % fs
stop = self.doubleSpinBox_5.value()
settings += '<p>stop: <a href="self.MACSE_exe doubleSpinBox_5.setFocus() doubleSpinBox_5.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_5)">%s</a></p>' % stop
local_realign_dec = self.doubleSpinBox_11.value()
settings += '<p>local_realign_dec: <a href="self.MACSE_exe doubleSpinBox_11.setFocus() doubleSpinBox_11.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_11)">%s</a></p>' % local_realign_dec
local_realign_init = self.doubleSpinBox_12.value()
settings += '<p>local_realign_init: <a href="self.MACSE_exe doubleSpinBox_12.setFocus() doubleSpinBox_12.selectAll()' \
' factory.highlightWidgets(x.doubleSpinBox_12)">%s</a></p>' % local_realign_init
max_refine_iter = self.spinBox.value()
settings += '<p>max_refine_iter: <a href="self.MACSE_exe spinBox.setFocus() spinBox.selectAll()' \
' factory.highlightWidgets(x.spinBox)">%s</a></p>' % max_refine_iter
optimization = self.comboBox_2.currentText()
settings += '<p>Optimization: <a href="self.MACSE_exe comboBox_2.showPopup()' \
' factory.highlightWidgets(x.comboBox_2)">%s</a></p>' % optimization
score_matrix = self.comboBox_3.currentText()
settings += '<p>Score matrix: <a href="self.MACSE_exe comboBox_3.showPopup()' \
' factory.highlightWidgets(x.comboBox_3)">%s</a></p>' % score_matrix
thread = self.comboBox_6.currentText()
settings += '<p>Thread: <a href="self.MACSE_exe comboBox_6.showPopup()' \
' factory.highlightWidgets(x.comboBox_6)">%s</a></p>' % thread
return settings
def isFileIn(self):
if self.checkBox_2.isChecked():
return self.comboBox_7.count()
else:
return self.comboBox_4.count()
def controlRefineText(self, bool_):
if bool_:
if not self.comboBox_7.count():
self.comboBox_7.lineEdit().switchColor(
"No input MSA (Improves previously computed alignments)")
else:
self.comboBox_7.lineEdit().switchColor()
else:
self.comboBox_7.lineEdit().switchColor()
def popup_MACSE_exception(self, text):
QMessageBox.critical(
self, "MACSE",
"<p style='line-height:25px; height:25px'>%s</p>" % text)
if "Show log" in text:
self.on_pushButton_9_clicked()
def replaceSymbols(self, list_results):
'''
替换结果里面的！和*
:return:
'''
for num, file in enumerate(list_results):
with open(file, encoding="utf-8", errors="ignore") as f:
content = f.read()
name, ext = os.path.splitext(file)
with open("%s_removed_chars%s" % (name, ext),
"w",
encoding="utf-8") as f1:
f1.write(content.replace("!", "?").replace("*", "?"))
self.progressSig.emit(95 + (5 * (num + 1) / len(list_results)))
self.workflow_progress.emit(95 + (5 *
(num + 1) / len(list_results)))