class PartitionEditor(QDialog, Ui_Partition_editor, object):
'''
局限性：三联密码子位置必须紧挨着，不能散布
'''
guiCloseSig = pyqtSignal(str)
def __init__(self, mode="PF2", parent=None):
self.factory = Factory()
self.thisPath = self.factory.thisPath
super(PartitionEditor, self).__init__(parent)
# 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.resize(400, 600)
self.setWindowFlags(self.windowFlags() | Qt.WindowMinMaxButtonsHint)
self.setupUi(self)
self.header = ["Name", "", "Start", "", "Stop"]
self.pushButton_2.clicked.connect(self.addRow)
self.pushButton.clicked.connect(self.deleteRow)
self.pushButton_recog.clicked.connect(self.recogFromText)
self.pushButton_codon.clicked.connect(self.ToCodonMode)
self.pushButton_nocodon.clicked.connect(self.CancelCodonMode)
self.data_type = "NUC"
self.mode = mode
## brief demo
country = self.factory.path_settings.value("country", "UK")
url = "http://phylosuite.jushengwu.com/dongzhang0725.github.io/documentation/#5-10-2-Brief-tutorial-for-partition-editor" if \
country == "China" else "https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#5-10-2-Brief-tutorial-for-partition-editor"
self.label_4.clicked.connect(
lambda: QDesktopServices.openUrl(QUrl(url)))
def readPartition(self, partition_content, mode="PF2"):
'''
:param partition_content: 串联生成的分区文件
:return: tableview的矩阵
'''
rgx = re.compile(r"(.+) *= *(\d+) *\- *(\d+)(\\3)?;") if mode == "PF2" \
else re.compile(r"charset (.+) *= *(\d+) *\- *(\d+)(\\3)?;")
list_contents = partition_content.split("\n")
arraydata = []
for line in list_contents:
if rgx.search(line):
geneName, start, stop, codonSite = rgx.findall(line)[0]
geneName_new = self.factory.refineName(geneName.strip(),
remain_words="-")
arraydata.append(
[geneName_new, "=", start, "-", stop + codonSite])
return arraydata
def readPartitionFromText(self, partition_content):
'''
从文本识别分区，先识别PF2格式的，如果没有再识别nex格式的
:param partition_content: 分区文本
:return: tableview的矩阵
'''
rgx1 = re.compile(r"(.+) *= *(\d+) *\- *(\d+)(\\3)?;")
rgx2 = re.compile(r"charset (.+) *= *(\d+) *\- *(\d+)(\\3)?;")
list_contents = partition_content.split("\n")
arraydata = []
for line in list_contents:
if rgx1.search(line):
geneName, start, stop, codonSite = rgx1.findall(line)[0]
geneName_new = self.factory.refineName(geneName.strip(),
remain_words="-")
arraydata.append(
[geneName_new, "=", start, "-", stop + codonSite])
elif rgx2.search(line):
geneName, start, stop, codonSite = rgx2.findall(line)[0]
geneName_new = self.factory.refineName(geneName.strip(),
remain_words="-")
arraydata.append(
[geneName_new, "=", start, "-", stop + codonSite])
return arraydata
def partition2text(self, arraydata, mode="PF2"):
'''
:param arraydata:
:return: partition文本，用于界面展示
'''
array = self.trimArray(arraydata)
if array:
self.GeneIndexIsOK(array)
if mode == "PF2":
return ";\n".join(["".join(i) for i in array]) + ";"
else:
return "#nexus\nbegin sets;\n%send;\n" % (
";\n".join(["charset " + "".join(i)
for i in array]) + ";\n")
else:
return ""
def addRow(self):
"""
add row
"""
currentModel = self.tableView_partition.model()
# print(currentModel.CDS_rows)
if currentModel:
currentData = currentModel.arraydata
currentModel.layoutAboutToBeChanged.emit()
list_data = []
for i in currentData[-1]:
if i in ["=", "-", " "]:
list_data.append(i)
else:
list_data.append("")
currentData.append(list_data)
currentModel.layoutChanged.emit()
# self.partitionDataSig.emit(currentData)
self.tableView_partition.scrollToBottom()
def deleteRow(self):
"""
delete row
"""
indices = self.tableView_partition.selectedIndexes()
if indices:
rows = sorted(set(index.row() for index in indices), reverse=True)
self.deleteFromRows(rows)
def deleteFromRows(self, rows):
currentModel = self.tableView_partition.model()
if currentModel:
currentData = currentModel.arraydata
for row in rows:
currentModel.layoutAboutToBeChanged.emit()
currentData.pop(row)
currentModel.layoutChanged.emit()
self.tableView_partition.clearSelection()
def refreshTableView(self, array, header):
model = MyPartEditorTableModel(array, header, parent=self)
model.dataChanged.connect(self.sortGenes)
self.tableView_partition.setModel(model)
def ctrlResizedColumn(self):
for j in range(0, 5):
self.tableView_partition.horizontalHeader().setSectionResizeMode(
j, QHeaderView.ResizeToContents)
def recogFromText(self):
text = self.textEdit.toPlainText()
array = self.readPartitionFromText(text)
if array:
reply = QMessageBox.question(
self, "Partition editor",
"This will overwrite the partitions in the above table and cannot be undone, continue?",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Yes:
model = MyPartEditorTableModel(array, self.header, parent=self)
model.dataChanged.connect(self.sortGenes)
self.tableView_partition.setModel(model)
self.ctrlResizedColumn() # 先执行一次改变列的宽度
else:
QMessageBox.information(
self, "Partition editor",
"<p style='line-height:25px; height:25px'>The format of the partition text cannot be recognized! "
"Hover mouse over the text box to see example.</p>")
def closeEvent(self, e):
currentModel = self.tableView_partition.model()
text = self.partition2text(currentModel.arraydata, mode=self.mode)
self.guiCloseSig.emit(text)
def trimArray(self, arraydata):
'''
只保留有值的array
:param arraydata:
:return:
'''
array = []
for i in arraydata:
if i[0] and i[2] and i[4]:
array.append(i)
return array
def ToCodonMode(self):
indices = self.tableView_partition.selectedIndexes()
currentModel = self.tableView_partition.model()
if currentModel and indices:
currentData = currentModel.arraydata
rows = sorted(set(index.row() for index in indices), reverse=True)
# 排除/3的行
CDS_rows = self.fetchCDSrow(currentData)
intersect_rows = list(set(rows).intersection(set(CDS_rows)))
if intersect_rows:
new_array = []
for row, line in enumerate(currentData):
if row in intersect_rows:
name, x1, start, x2, stop = line
new_array.append(
[name + "_codon1", "=", start, "-", stop + "\\3"])
new_array.append([
name + "_codon2", "=",
str(int(start) + 1), "-", stop + "\\3"
])
new_array.append([
name + "_codon3", "=",
str(int(start) + 2), "-", stop + "\\3"
])
else:
new_array.append(line)
model = MyPartEditorTableModel(new_array,
self.header,
parent=self)
model.dataChanged.connect(self.sortGenes)
self.tableView_partition.setModel(model)
self.ctrlResizedColumn()
else:
QMessageBox.information(
self, "Partition editor",
"<p style='line-height:25px; height:25px'>The length of the selected genes is not a multiple of 3 or "
"the data are already in the codon mode!</p>")
def CancelCodonMode(self):
'''
3个位点都选中的时候，才能取消，如果没有选中要说明一下
:return:
'''
indices = self.tableView_partition.selectedIndexes()
currentModel = self.tableView_partition.model()
if currentModel and indices:
currentData = currentModel.arraydata
rows = sorted(set(index.row() for index in indices), reverse=True)
dict_ = {} # {789: [1, 2, 3]} #stop位置及其所有起始位置
for row in rows:
if "\\3" in currentData[row][4]:
start = int(currentData[row][2])
stop = int(currentData[row][4].replace("\\3", ""))
dict_.setdefault(stop, ["NA", "NA", "NA"])
# 不管是哪一位，先把三联的起始位置找到
if (stop - start + 1) % 3 == 0: dict_[stop][0] = row #第一位
elif (stop - start + 1) % 3 == 2:
dict_[stop][1] = row #第二位
elif (stop - start + 1) % 3 == 1:
dict_[stop][2] = row # 第三位
#先按三联行的位置排序，然后从大开始删和修改
list_values = sorted([i for i in dict_.values() if "NA" not in i],
key=lambda x: max(x),
reverse=True)
for i in list_values:
delete_rows = sorted(i, reverse=True)
if delete_rows:
# 先修改第一个
currentModel.layoutAboutToBeChanged.emit()
currentData[delete_rows[-1]][0] = re.sub(
r"_codon\d", "", currentData[delete_rows[0]][0])
currentData[delete_rows[-1]][4] = currentData[
delete_rows[0]][4].replace("\\3", "")
currentModel.layoutChanged.emit()
self.deleteFromRows(delete_rows[:-1]) #只删除2、3行
self.ctrlResizedColumn()
def fetchCDSrow(self, array):
CDS_rows = []
for row, line in enumerate(array):
if "\\3" in line[4]: continue
start = int(line[2])
stop = int(line[4].replace("\\3", ""))
if (stop - start + 1) % 3 == 0:
if row not in CDS_rows: CDS_rows.append(row)
return CDS_rows
def showEvent(self, event):
self.textEdit.clear()
def sortGenes(self):
self.tableView_partition.sortByColumn(2, Qt.AscendingOrder)
def GeneIndexIsOK(self, array):
# 基因多的时候只展示前2个
list_ = [] # [[cox1, 1, 867]]
for row in array:
geneName, start, stop = row[0], int(row[2]), int(row[4].replace(
"\\3", ""))
if "\\3" in row[4]:
if ((stop - start + 1) % 3 == 0):
list_.append([geneName, start, stop])
else:
list_.append([geneName, start, stop])
overlap = [] # [[cox1, cox2]]
space = [] # [[cox1, cox2]]
startError = ""
last = None
for i in list_:
if last:
diff = i[1] - last[2] - 1
if diff < 0:
overlap.append([last[0], i[0]])
elif diff > 0:
space.append([last[0], i[0]])
else:
# 起始位置
if i[1] != 1:
# 起始必须是1开始
startError = " <span style='font-weight:600'>*</span> <span style='font-weight:600; color:#ff0000;'>%s</span> must start with 1.<br>" % i[
0]
last = i
error = ""
if startError: error += startError
if overlap:
if len(overlap) > 2:
overlap_ = overlap[:2]
extra_text = "And %d more overlapping region(s)...<br><br>" % (
len(overlap) - 2)
else:
overlap_ = overlap
extra_text = ""
text = "".join([
" <span style='font-weight:600'>*</span> Positions overlapped between <span style='font-weight:600; color:#ff0000;'>%s</span> and <span style='font-weight:600; color:#ff0000;'>%s</span><br>"
% (j[0], j[1]) for j in overlap_
])
error += text + extra_text
if space:
if len(overlap) > 2:
space_ = space[:2]
extra_text = "And %d more unassigned region(s)...<br><br>" % (
len(space) - 2)
else:
space_ = space
extra_text = ""
text = "".join([
" <span style='font-weight:600'>*</span> Unassigned positions found between <span style='font-weight:600; color:#ff0000;'>%s</span> and <span style='font-weight:600; color:#ff0000;'>%s</span><br>"
% (j[0], j[1]) for j in space_
])
error += text + extra_text
error = "Gene positions setting failed:<br>" + error if error else ""
if error:
QMessageBox.warning(
self, "Warning",
"<p style='line-height:25px; height:25px'>%s</p>" % error)
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 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.warning_message = ""
self.parsefmt = Parsefmt(self.error_message, self.warning_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]
geneName = self.factory.refineName(geneName)
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
self.warning_message += self.parsefmt.warning_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)
self.ok = False
return
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)
if self.warning_message:
QMetaObject.invokeMethod(self.parent, "popupWarning",
Qt.BlockingQueuedConnection,
Q_ARG(list, [self.warning_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(list, [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.warning_message += self.parsefmt.warning_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')
