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 Seq_matrix(object):
def __init__(self, **kwargs):
self.factory = Factory()
self.dict_args = kwargs
self.outpath = self.dict_args["exportPath"]
self.dict_species = {}
self.dict_statistics = dict(prefix='taxon')
self.partition_style = '***partitionfinder style***\n'
self.partition_codon = "\n***codon style***\n"
self.bayes_style = '\n***bayes style***\n'
self.bayes_codon = "\n***bayes codon style***\n"
self.iqtree_style = '\n***IQ-TREE style***\n#nexus\nbegin sets;\n'
self.iqtree_codon = "\n***IQ-TREE codon style***\n#nexus\nbegin sets;\n"
self.parent = self.dict_args["parent"]
self.partition_name = ''
self.partition_codname = ""
self.gene_index = []
self.dist_warning_message = OrderedDict()
self.error_message = ""
self.parsefmt = Parsefmt(self.error_message)
self.dict_genes_alignments = OrderedDict()
self.unaligned = False
self.unaligns = []
self.exportName = self.dict_args["export_name"]
self.interrupt = False
self.list_empty_files = []
for num, eachFile in enumerate(self.dict_args["files"]):
if self.interrupt:
break
geneName = os.path.splitext(os.path.basename(eachFile))[0]
dict_taxon = self.parsefmt.readfile(eachFile)
set_length = set([len(dict_taxon[i]) for i in dict_taxon])
if set_length == {0}:
self.list_empty_files.append(os.path.basename(eachFile))
continue
self.error_message += self.parsefmt.error_message
if self.factory.is_aligned(dict_taxon):
self.dict_genes_alignments[geneName] = dict_taxon
else:
self.unaligned = True
self.unaligns.append(geneName)
if self.list_empty_files:
if len(self.list_empty_files) == 1:
text = "The empty file \"%s\" will be ignored" % self.list_empty_files[
0]
else:
file_names = "\", \"".join(
self.list_empty_files[:-1]
) + "\" and \"%s\"" % self.list_empty_files[-1]
text = "The empty files \"%s will be ignored" % file_names
QMetaObject.invokeMethod(self.parent, "popupEmptyFileWarning",
Qt.BlockingQueuedConnection,
Q_ARG(str, text))
if self.unaligned:
self.dict_args["unaligned_signal"].emit(self.unaligns)
if self.dict_genes_alignments:
self.supplement()
self.concatenate()
self.ok = True
else:
self.ok = False
def concatenate(self):
total = len(self.dict_args["files"])
self.dict_args["progressSig"].emit(10)
self.dict_args["workflow_progress"].emit(10)
if not self.unaligned: # 确认比对过
for num, self.genename in enumerate(self.dict_genes_alignments):
if self.interrupt:
break
self.dict_taxon = self.dict_genes_alignments[self.genename]
self.dict_statistics['prefix'] += '\t' + self.genename
self.append()
self.addPartition()
self.dict_args["progressSig"].emit(10 +
((num + 1) * 80 / total))
self.dict_args["workflow_progress"].emit(10 + (
(num + 1) * 80 / total))
if self.interrupt:
return
self.complete() # 完善
self.save() # 存档
self.dict_args["progressSig"].emit(100)
self.dict_args["workflow_progress"].emit(100)
if self.error_message:
self.dict_args["exception_signal"].emit(self.error_message)
# else:
# self.dict_args["unaligned_signal"].emit(self.unaligns)
def supplement(self):
# 补全缺失基因的物种
# dict_maxTaxa = max(*[self.dict_genes_alignments[i]
# for i in self.dict_genes_alignments], key=len) # 物种数最多的基因
dict_maxTaxa = []
for k in self.dict_genes_alignments:
if self.interrupt:
break
list_taxon = list(self.dict_genes_alignments[k].keys())
dict_maxTaxa.extend(list_taxon)
list_set_dict_maxTaxa = list(set(dict_maxTaxa))
for i in list_set_dict_maxTaxa:
if self.interrupt:
break
lossingGene = []
for j in self.dict_genes_alignments:
if self.interrupt:
break
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:
self.dist_warning_message[i] = lossingGene
if self.dist_warning_message:
##报错
QMetaObject.invokeMethod(
self.parent, "popupWarning", Qt.BlockingQueuedConnection,
Q_ARG(OrderedDict, self.dist_warning_message))
def append(self):
for self.spe_key, self.seq in self.dict_taxon.items(): # 因为读新的文件会
self.seq = self.seq.upper() # 全部改为大写
lenth = len(self.seq)
indels = self.seq.count('-')
if self.spe_key in self.dict_species:
self.dict_species[self.spe_key] += self.seq
if self.spe_key in self.dict_statistics:
self.dict_statistics[self.spe_key] += '\t' + \
str(lenth) + ' (' + str(indels) + ' indels)'
else:
self.dict_statistics[self.spe_key] = '\t' + \
str(lenth) + ' (' + str(indels) + ' indels)'
else:
self.dict_species[self.spe_key] = self.seq
self.dict_statistics[self.spe_key] = self.spe_key + \
'\t' + str(lenth) + ' (' + str(indels) + ' indels)'
def addPartition(self):
##替换这些特殊符号，可以让序列更容易被识别
rgx = re.compile(r"([.^$*+?{}[\]\\|()])")
matFlag = rgx.sub(r"[\1]", self.seq) + '$'
span = re.search(matFlag, self.dict_species[self.spe_key]).span()
self.gene_index.append(span)
self.partition_style += self.genename + '=' + \
str(span[0] + 1) + '-' + str(span[1]) + ';\n'
self.partition_codon += self.genename + "_codon1" + \
'=' + str(span[0] + 1) + '-' + str(span[1]) + '\\3;\n'
self.partition_codon += self.genename + "_codon2" + \
'=' + str(span[0] + 2) + '-' + str(span[1]) + '\\3;\n'
self.partition_codon += self.genename + "_codon3" + \
'=' + str(span[0] + 3) + '-' + str(span[1]) + '\\3;\n'
self.bayes_style += 'charset ' + self.genename + \
'=' + str(span[0] + 1) + '-' + str(span[1]) + ';\n'
self.bayes_codon += 'charset ' + self.genename + "_codon1" + \
'=' + str(span[0] + 1) + '-' + str(span[1]) + '\\3;\n'
self.bayes_codon += 'charset ' + self.genename + "_codon2" + \
'=' + str(span[0] + 2) + '-' + str(span[1]) + '\\3;\n'
self.bayes_codon += 'charset ' + self.genename + "_codon3" + \
'=' + str(span[0] + 3) + '-' + str(span[1]) + '\\3;\n'
self.iqtree_style += '\tcharset ' + self.genename + \
'=' + str(span[0] + 1) + '-' + str(span[1]) + ';\n'
self.iqtree_codon += '\tcharset ' + self.genename + "_codon1" + \
'=' + str(span[0] + 1) + '-' + str(span[1]) + '\\3;\n'
self.iqtree_codon += '\tcharset ' + self.genename + "_codon2" + \
'=' + str(span[0] + 2) + '-' + str(span[1]) + '\\3;\n'
self.iqtree_codon += '\tcharset ' + self.genename + "_codon3" + \
'=' + str(span[0] + 3) + '-' + str(span[1]) + '\\3;\n'
self.partition_name += self.genename + ','
self.partition_codname += self.genename + "_codon1," + \
self.genename + "_codon2," + self.genename + "_codon3,"
def align(self, seq):
list_seq = re.findall(r'(.{60})', seq)
if not list_seq:
return seq + "\n"
remainder = len(seq) % 60
if remainder == 0:
self.align_seq = '\n'.join(list_seq) + '\n'
else:
self.align_seq = '\n'.join(
list_seq) + '\n' + seq[-remainder:] + '\n'
def nxs_interleave(self):
length = len(self.dict_species[self.list_keys[-1]]) # 总长
integer = length // 60
num = 1
if self.dict_args["export_nexi"]:
while num <= integer:
for i in self.list_keys:
self.nxs_inter += i.ljust(
self.name_longest) + ' ' + self.dict_species[i][
(num - 1) * 60:num * 60] + '\n'
self.nxs_inter += "\n"
num += 1
if length % 60 != 0:
for i in self.list_keys:
self.nxs_inter += i.ljust(
self.name_longest) + ' ' + self.dict_species[i][
(num - 1) * 60:length] + '\n'
if self.dict_args["export_nexig"]:
for each_span in self.gene_index: # 以gene分界形式的nex
for i in self.list_keys:
self.nxs_gene += i.ljust(
self.name_longest) + " " + self.dict_species[i][
each_span[0]:each_span[1]] + "\n"
self.nxs_gene += "\n"
def get_str(self): # 只有nex和phy格式需要改序列名字空格
for i in self.list_keys:
self.dict_statistics[i] += '\t' + \
str(len(self.dict_species[i])) + '\t' + str(self.count) + '\n'
self.file += '>' + i + '\n' + \
self.dict_species[i] + '\n'
self.phy_file += i.ljust(self.name_longest) + \
' ' + self.dict_species[i] + '\n'
self.nxs_file += i.ljust(self.name_longest) + \
' ' + self.dict_species[i] + '\n'
self.align(self.dict_species[i])
self.paml_file += i + '\n' + \
self.align_seq + '\n'
self.axt_file += self.dict_species[i] + '\n'
self.statistics += self.dict_statistics[i]
def complete(self):
self.count = len(self.dict_genes_alignments)
self.partition_name = 'partition Names = %s:' % str(
self.count) + self.partition_name.strip(
',') + ';\nset partition=Names;\n'
self.partition_codname = 'partition Names = %s:' % str(
self.count * 3) + self.partition_codname.strip(
',') + ';\nset partition=Names;\n'
self.dict_statistics['prefix'] += '\tTotal lenth\tNo of charsets\n'
self.list_keys = sorted(list(self.dict_species.keys()))
self.pattern = self.parsefmt.which_pattern(
self.dict_species, "Concatenated file") # 得到pattern
self.error_message += self.parsefmt.error_message
self.file = ''
self.phy_file = ' ' + \
str(len(self.list_keys)) + ' ' + \
str(len(self.dict_species[self.list_keys[-1]])) + '\n'
self.nxs_file = '#NEXUS\nBEGIN DATA;\ndimensions ntax=%s nchar=%s;\nformat missing=?\ndatatype=%s gap= -;\n\nmatrix\n' % (
str(len(self.list_keys)),
str(len(self.dict_species[self.list_keys[-1]])), self.pattern)
self.nxs_inter = '#NEXUS\nBEGIN DATA;\ndimensions ntax=%s nchar=%s;\nformat missing=?\ndatatype=%s gap= - interleave;\n\nmatrix\n' % (
str(len(self.list_keys)),
str(len(self.dict_species[self.list_keys[-1]])), self.pattern)
'''nex的interleave模式'''
self.nxs_gene = '#NEXUS\nBEGIN DATA;\ndimensions ntax=%s nchar=%s;\nformat missing=?\ndatatype=%s gap= - interleave;\n\nmatrix\n' % (
str(len(self.list_keys)),
str(len(self.dict_species[self.list_keys[-1]])), self.pattern)
'''nex的interleave模式，以gene换行'''
self.paml_file = str(len(self.list_keys)) + ' ' + \
str(len(self.dict_species[self.list_keys[-1]])) + '\n\n'
self.axt_file = '-'.join(self.list_keys) + '\n'
self.statistics = self.dict_statistics['prefix']
list_lenth = [len(i) for i in self.list_keys]
self.name_longest = max(list_lenth) # 最长的序列名字
self.get_str()
self.nxs_interleave()
def save(self):
self.partition_detail = self.outpath + os.sep + 'partition.txt'
with open(self.partition_detail, 'w', encoding="utf-8") as f4:
f4.write(self.partition_style + self.partition_codon +
self.bayes_style + self.partition_name +
self.bayes_codon + self.partition_codname +
self.iqtree_style + "end;\n" + self.iqtree_codon + "end;")
if self.dict_args["export_axt"]:
with open(self.outpath + os.sep + '%s.axt' % self.exportName,
'w',
encoding="utf-8") as f1:
f1.write(self.axt_file)
if self.dict_args["export_fas"]:
with open(self.outpath + os.sep + '%s.fas' % self.exportName,
'w',
encoding="utf-8") as f2:
f2.write(self.file)
if self.dict_args["export_stat"]:
with open(self.outpath + os.sep + 'statistics.csv',
'w',
encoding="utf-8") as f3:
f3.write(self.statistics.replace('\t', ','))
if self.dict_args["export_phylip"]:
with open(self.outpath + os.sep + '%s.phy' % self.exportName,
'w',
encoding="utf-8") as f5:
f5.write(self.phy_file)
if self.dict_args["export_nex"]:
with open(self.outpath + os.sep + '%s.nex' % self.exportName,
'w',
encoding="utf-8") as f6:
f6.write(self.nxs_file + ';\nEND;\n')
if self.dict_args["export_paml"]:
with open(self.outpath + os.sep + '%s.PML' % self.exportName,
'w',
encoding="utf-8") as f7:
f7.write(self.paml_file)
if self.dict_args["export_nexi"]:
with open(self.outpath + os.sep +
'%s_interleave.nex' % self.exportName,
'w',
encoding="utf-8") as f8:
f8.write(self.nxs_inter + ';\nEND;\n')
if self.dict_args["export_nexig"]:
with open(self.outpath + os.sep +
'%s_bygene.nex' % self.exportName,
'w',
encoding="utf-8") as f9:
f9.write(self.nxs_gene + ';\nEND;\n')
