#!/usr/bin/env python
# -*- coding: utf-8 -*-
# 自己调整好一个size，然后再guirestore恢复一下
import datetime
import glob
import re
import multiprocessing
import signal
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
from uifiles.Ui_HmmCleaner import Ui_HmmCleaner
from src.factory import Factory, WorkThread
import inspect
import os
import sys
import traceback
import subprocess
import platform
from multiprocessing.pool import ApplyResult
def run(dict_args, command, file):
fileBase = os.path.basename(file)
inputFile = " \"%s\"" % file
command = command.replace(" $alignment$", inputFile) #html输出替换名字
startupINFO = None
if platform.system().lower() == "windows":
startupINFO = subprocess.STARTUPINFO()
startupINFO.dwFlags |= subprocess.STARTF_USESHOWWINDOW
startupINFO.wShowWindow = subprocess.SW_HIDE
popen = subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, startupinfo=startupINFO)
else:
popen = subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, startupinfo=startupINFO, shell=True,
preexec_fn=os.setsid)
run.queue.put(("popen", popen.pid))
# 存log文件
with open(file + ".log", "a", encoding="utf-8") as log_file:
run.queue.put(("log", "%sCommands%s\n%s\n%s" % ("=" * 45, "=" * 45, command, "=" * 98)))
is_error = False
while True:
try:
out_line = popen.stdout.readline().decode("utf-8", errors='ignore')
except UnicodeDecodeError:
out_line = popen.stdout.readline().decode("gbk", errors='ignore')
if out_line == "" and popen.poll() is not None:
break
if re.search(r"\S+", out_line):
log_file.write(out_line)
run.queue.put(("log", fileBase + " --- " + out_line.strip()))
if re.search(r"ERROR", out_line):
run.queue.put(("log", fileBase + " --- " + out_line.strip()))
is_error = True
if is_error:
run.queue.put(("error",))
else:
pass
run.queue.put(("prog", "finished"))
run.queue.put(("log", fileBase + " --- " + "Done!"))
run.queue.put(("popen finished", popen.pid))
return "finished"
def pool_init(queue):
# see http://stackoverflow.com/a/3843313/852994
run.queue = queue
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)
##弹出识别输入文件的信号
auto_popSig = pyqtSignal(QDialog)
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.function_name = "HmmCleaner"
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")))
##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_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., 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 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.factory.centerWindow(self)
# 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 dongzhang0725@gmail.com')
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)
with open(self.exportPath + os.sep + "PhyloSuite_HmmCleaner.log", "a") as f:
f.write(text + "\n")
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, init=False):
self.init = init
self.factory.popUpAutoDetect("HmmCleaner", 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):
'''* 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()
if __name__ == "__main__":
app = QApplication(sys.argv)
ui = HmmCleaner()
ui.show()
sys.exit(app.exec_())
