class Lg_addFiles(QDialog, Ui_addFile, object):
closeGUI_signal = pyqtSignal()
inputSig = pyqtSignal(list, list, bool, str)
inputContentSig = pyqtSignal(str, str)
exception_signal = pyqtSignal(str)
progressDiologSig = pyqtSignal(int)
fastaDownloadFinishedSig = pyqtSignal(str)
inputFasSig = pyqtSignal(str, str)
def __init__(self, exportPath=None, parent=None):
super(Lg_addFiles, self).__init__(parent)
self.factory = Factory()
self.parent = parent
self.thisPath = self.factory.thisPath
self.exportPath = exportPath
# 保存设置
self.addFiles_settings = QSettings(
self.thisPath +
'/settings/addFiles_settings.ini',
QSettings.IniFormat)
self.closeGUI_signal.connect(self.close)
self.progressDiologSig.connect(self.runProgressDialog)
# self.close() 不能在信号槽里面
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss', encoding="utf-8", errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
self.setupUi(self)
self.guiRestore()
self.exception_signal.connect(self.popupException)
self.interrupt = False
self.label_3.clicked.connect(lambda : QDesktopServices.openUrl(QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-1-1-Brief-example")))
def fetSeqFromNCBI(self, id_array):
batch_size = 20
count = len(id_array)
download_contents = ""
for start in range(0, count, batch_size):
if self.interrupt:
return
end = min(count, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > count:
batch_size = count - start
Entrez.email = self.email if self.email else "*****@*****.**"
fetch_handle = Entrez.efetch(db="nucleotide", rettype=self.rettype, retmode="text",
retstart=start, retmax=batch_size, id=id_array)
download_contents += fetch_handle.read()
self.progressDiologSig.emit(end * 100 / count)
if self.rettype == "gb":
self.inputContentSig.emit(
download_contents, self.outputPath)
else:
with open(self.outputPath + os.sep + self.fasta_file_name, "w", encoding="utf-8") as f:
f.write(download_contents)
self.fastaDownloadFinishedSig.emit(self.outputPath)
# result_handle = Entrez.efetch(
# db="nucleotide", rettype="gb", id=id_array, retmode="text")
# # with open(self.exportPath + os.sep + "new.gb", "w", encoding="utf-8") as f2:
# # f2.write(result_handle.read())
# self.inputContentSig.emit(
# result_handle.read(), [])
@pyqtSlot()
def on_pushButton_clicked(self):
self.outputPath = self.fetchOutputPath()
if self.parent.isWorkFolder(self.outputPath, mode="gb"):
files = QFileDialog.getOpenFileNames(
self, "Input GenBank Files", filter="GenBank and Fasta Format (*.gb *.gbk *.gbf *.gp *.gbff *.fas *.fasta);;")
if files[0]:
list_gbs = []
list_fas = []
for i in files[0]:
if os.path.splitext(i)[1].upper() in [".GB", ".GBK", ".GP", ".GBF", ".GBFF"]:
list_gbs.append(i)
elif os.path.splitext(i)[1].upper() in [".FAS", ".FASTA"]:
list_fas.append(i)
if list_gbs:
self.inputSig.emit(list_gbs, [], False, self.outputPath)
if list_fas:
fasContent = ""
for i in list_fas:
with open(i, encoding="utf-8", errors='ignore') as f:
fasContent += f.read() + "\n"
self.inputFasSig.emit(fasContent, self.outputPath)
self.close()
self.deleteLater()
del self
else:
files = QFileDialog.getOpenFileNames(
self, "Input Files",
filter="Supported Format (*.docx *.doc *.odt *.docm *.dotx *.dotm *.dot "
"*.fas *.fasta *.phy *.phylip *.nex *.nxs *.nexus);;")
if files[0]:
self.inputSig.emit([], files[0], False, self.outputPath)
self.close()
self.deleteLater()
del self
@pyqtSlot()
def on_pushButton_2_clicked(self):
# download
self.interrupt = False
text_content = self.plainTextEdit.toPlainText()
if text_content:
self.outputPath = self.fetchOutputPath()
self.rettype = "gb" if self.parent.isWorkFolder(self.outputPath, mode="gb") else "fasta"
if self.rettype == "fasta":
name, ok = QInputDialog.getText(
self, 'Set output file name', 'Output file name:', text="sequence.fas")
if ok:
self.fasta_file_name = name + ".fas" if "." not in name else name
if os.path.exists(self.outputPath + os.sep + self.fasta_file_name):
reply = QMessageBox.question(
self,
"Concatenate sequence",
"<p style='line-height:25px; height:25px'>The file exists, replace it?</p>",
QMessageBox.Yes,
QMessageBox.Cancel)
if reply == QMessageBox.Cancel:
return
else:
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>Download canceled!</p>")
return
self.downloadState("start")
self.progressDialog = self.factory.myProgressDialog(
"Please Wait", "Downloading...", parent=self)
self.progressDialog.show()
self.id_array = re.split(r"\s|,", text_content)
while "" in self.id_array:
self.id_array.remove("")
self.email = self.lineEdit.text()
self.worker_download = WorkThread(self.run_command, parent=self)
self.progressDialog.canceled.connect(lambda: [setattr(self, "interrupt", True),
self.worker_download.stopWork(),
self.progressDialog.close(),
self.downloadState("stop")])
self.worker_download.start()
else:
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>Please input ID(s) first</p>")
@pyqtSlot()
def on_pushButton_8_clicked(self):
#search in NCBI
self.close()
self.parent.on_SerhNCBI_triggered()
@pyqtSlot()
def on_toolButton_clicked(self):
info = '''To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request.<br>
In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities.'''
QMessageBox.information(
self,
"Information",
"<p style='line-height:25px; height:25px'>%s</p>"%info)
def run_command(self):
try:
self.fetSeqFromNCBI(self.id_array)
self.closeGUI_signal.emit()
except BaseException:
self.exceptionInfo = ''.join(
traceback.format_exception(
*sys.exc_info())) # 捕获报错内容，只能在这里捕获，没有报错的地方无法捕获
self.exception_signal.emit(self.exceptionInfo)
# self.popupException(self.exceptionInfo) # 激发这个信号
def popupException(self, exception):
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(
'The program encountered an unforeseen problem, please report the bug at <a href="https://github.com/dongzhang0725/PhyloSuite/issues">https://github.com/dongzhang0725/PhyloSuite/issues</a> or send an email with the detailed traceback to [email protected]')
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
self.pushButton_2.setEnabled(True)
self.pushButton_2.setStyleSheet(self.qss_file)
self.pushButton_2.setText("Start")
def guiSave(self):
# Save geometry
self.addFiles_settings.setValue('size', self.size())
# self.addFiles_settings.setValue('pos', self.pos())
# for name, obj in inspect.getmembers(self):
# if type(obj) is QComboBox: # this works similar to isinstance, but
# missed some field... not sure why?
# if isinstance(obj, QTextBrowser):
# # save combobox selection to registry
# htmlText = obj.toHtml()
# self.addFiles_settings.setValue(name, htmlText)
def guiRestore(self):
# Restore geometry
self.resize(self.addFiles_settings.value('size', QSize(500, 500)))
# self.move(self.addFiles_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox":
allItems = self.factory.fetchAllWorkFolders(self.exportPath)
model = obj.model()
obj.clear()
for num, i in enumerate(allItems):
if self.parent.isWorkFolder(i, mode="gb"):
text = "\"%s\" in GenBank_File (GenBank format)"%os.path.basename(i)
else:
text = "\"%s\" in Other_File" % os.path.basename(i)
item = QStandardItem(text)
item.setToolTip(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
if self.parent.isWorkFolder(self.exportPath, mode="gb"):
obj.setCurrentText("\"%s\" in GenBank_File (GenBank format)"%os.path.basename(self.exportPath))
else:
obj.setCurrentText("\"%s\" in Other_File" % os.path.basename(self.exportPath))
def closeEvent(self, event):
self.interrupt = True
if hasattr(self, "worker_download"):
self.worker_download.stopWork()
if hasattr(self, "progressDialog"):
self.progressDialog.close()
self.guiSave()
def runProgressDialog(self, num):
oldValue = self.progressDialog.value()
done_int = int(num)
if done_int > oldValue:
self.progressDialog.setProperty("value", done_int)
QCoreApplication.processEvents()
if done_int == 100:
self.progressDialog.close()
def fetchOutputPath(self):
index = self.comboBox.currentIndex()
return self.comboBox.itemData(index, role=Qt.ToolTipRole)
def downloadState(self, state):
if state == "start":
self.pushButton_2.setEnabled(False) # 使之失效
self.pushButton_2.setStyleSheet(
'QPushButton {color: red; background-color: rgb(219, 217, 217)}')
self.pushButton_2.setText("Downloading...")
elif state == "stop":
self.pushButton_2.setText("Download")
self.pushButton_2.setStyleSheet(self.qss_file)
self.pushButton_2.setEnabled(True)
class SerhNCBI(QMainWindow, Ui_SerhNCBI, object):
exception_signal = pyqtSignal(str) # 定义所有类都可以使用的信号
updateSig = pyqtSignal(list)
searchSig = pyqtSignal(str)
progressBarSig = pyqtSignal(int) # 控制进度条
progressDiologSig = pyqtSignal(int)
ctrlItemsSig = pyqtSignal(int)
inputContentSig = pyqtSignal(str, str)
downloadFinished = pyqtSignal()
fastaDownloadFinishedSig = pyqtSignal(str)
def __init__(self, workPath=None, parent=None):
super(SerhNCBI, self).__init__(parent)
# self.thisPath = os.path.dirname(os.path.realpath(__file__))
self.parent = parent
self.factory = Factory()
self.thisPath = self.factory.thisPath
self.workPath = workPath
self.setupUi(self)
# 保存设置
self.serhNCBI_settings = QSettings(
self.thisPath + '/settings/serhNCBI_settings.ini',
QSettings.IniFormat)
# File only, no fallback to registry or or.
self.serhNCBI_settings.setFallbacksEnabled(False)
# 开始装载样式表
with open(self.thisPath + os.sep + 'style.qss',
encoding="utf-8",
errors='ignore') as f:
self.qss_file = f.read()
self.setStyleSheet(self.qss_file)
# 恢复用户的设置
self.guiRestore()
self.exception_signal.connect(self.popupException)
# self.progressSig.connect(self.runProgress)
# self.logGuiSig.connect(self.addText2Log)
self.lineEdit.buttonSearch.clicked.connect(lambda: [
self.startSearch(),
self.sync_completer_texts(self.lineEdit.text())
])
self.lineEdit.buttonStop.clicked.connect(self.stopSearch)
# self.lineEdit.completer().popup().show()
# self.lineEdit.clicked.connect(lambda : self.lineEdit.completer().popup())
self.dict_ncbi_headers = {
"GBSeq_accession-version": "ID",
"GBSeq_definition": "Description",
"GBSeq_organism": "Organism",
"GBSeq_length": "Length",
"GBSeq_update-date": "Update date",
"GBSeq_taxonomy": "Taxonomy",
"GBSeq_create-date": "Create date",
"GBSeq_moltype": "Molecular type",
"GBSeq_topology": "Topology",
"GBSeq_references": "References",
"GBSeq_source": "Source",
"GBSeq_keywords": "Keywords",
"GBSeq_project": "Project",
"GBSeq_other-seqids": "Other IDs",
"GBSeq_strandedness": "Strandedness",
"GBSeq_comment": "Comments"
}
self.init_list()
self.updateSig.connect(self.updateTable)
self.searchSig.connect(self.ctrlSearchState)
self.progressBarSig.connect(self.searchProgress)
self.progressDiologSig.connect(self.runProgressDialog)
self.spinBox.valueChanged.connect(self.sync_display_items)
self.ctrlItemsSig.connect(self.ctrlItems)
# self.downloadFinished.connect(self.downloadDone)
self.fastaDownloadFinishedSig.connect(self.parent.setTreeViewFocus)
self.NCBI_model = MyNCBITableModel([self.list_table_header],
parent=self)
self.tableView.setModel(self.NCBI_model)
header = CheckBoxHeader(parent=self.tableView)
header.clicked.connect(self.check_displayed)
self.tableView.setHorizontalHeader(header)
self.NCBI_model.checkedChanged.connect(self.ctrl_text)
self.interrupt = False
##下载的状态
widget = QWidget(self)
horizBox = QHBoxLayout(widget)
horizBox.setContentsMargins(0, 0, 0, 0)
spacerItem = QSpacerItem(40, 20, QSizePolicy.Expanding,
QSizePolicy.Minimum)
self.disp_check_label = QLabel(
"<span style='font-weight:600; color:red;'>Searching...</span>",
self)
self.disp_check_gifLabel = QLabel(self)
movie = QMovie(":/picture/resourses/Spinner-1s-34px.gif")
self.disp_check_gifLabel.setMovie(movie)
self.disp_check_progress = QProgressBar(self)
self.disp_check_progress.setFixedWidth(100)
movie.start()
horizBox.addItem(spacerItem)
horizBox.addWidget(self.disp_check_gifLabel)
horizBox.addWidget(self.disp_check_label)
horizBox.addWidget(self.disp_check_progress)
self.statusbar.addPermanentWidget(widget)
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.installEventFilter(self)
self.spinBox.installEventFilter(self)
table_popMenu = QMenu(self)
table_popMenu.setToolTipsVisible(True)
OpenID = QAction(QIcon(":/seq_Viewer/resourses/field-Display.png"),
"Open in NCBI webpage",
self,
triggered=self.openID)
OpenID.setToolTip("Open sequence in NCBI webpage")
table_popMenu.addAction(OpenID)
def table_popmenu(qpoint):
if self.tableView.indexAt(qpoint).isValid():
table_popMenu.exec_(QCursor.pos())
self.tableView.setContextMenuPolicy(Qt.CustomContextMenu)
self.tableView.customContextMenuRequested.connect(table_popmenu)
# self.tableView.horizontalHeader().resizeSection(1, 300)
# self.tableView.horizontalHeader().resizeSection(2, 80)
# ##增加check按钮
# self.check_all = QCheckBox("Check/Uncheck", self)
# self.check_all.toggled.connect(self.check_displayed)
# self.statusbar.addWidget(self.check_all)
## brief demo
self.label_6.clicked.connect(lambda: QDesktopServices.openUrl(
QUrl(
"https://dongzhang0725.github.io/dongzhang0725.github.io/documentation/#4-3-3-1-Brief-example"
)))
@pyqtSlot()
def on_toolButton_clicked(self):
info = '''To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request.<br>
In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities.'''
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>%s</p>" % info)
@pyqtSlot()
def on_toolButton_2_clicked(self):
#refresh
self.interrupt = False
self.exist_base = self.NCBI_model.rowCount(self.tableView)
if not self.exist_base:
return
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
return
if self.display_items > self.exist_base:
self.worker_addition = WorkThread(self.addition_search,
parent=self)
self.worker_addition.start()
# elif self.display_items < self.exist_base:
# list_checked = self.NCBI_model.list_checked
# array = self.NCBI_model.array[:self.display_items+1]
# self.NCBI_model = MyNCBITableModel(array, list_checked, self.tableView)
# self.tableView.setModel(self.NCBI_model)
# self.tableView.update()
@pyqtSlot()
def on_toolButton_3_clicked(self):
# download
index = self.comboBox.currentIndex()
self.outputPath = self.comboBox.itemData(index, role=Qt.ToolTipRole)
self.rettype = "gb" if self.parent.isWorkFolder(self.outputPath,
mode="gb") else "fasta"
if self.rettype == "fasta":
name, ok = QInputDialog.getText(self,
'Set output file name',
'Output file name:',
text="sequence.fas")
if ok:
self.fasta_file_name = name + ".fas" if "." not in name else name
if os.path.exists(self.outputPath + os.sep +
self.fasta_file_name):
reply = QMessageBox.question(
self, "Concatenate sequence",
"<p style='line-height:25px; height:25px'>The file exists, replace it?</p>",
QMessageBox.Yes, QMessageBox.Cancel)
if reply == QMessageBox.Cancel:
return
else:
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>Download canceled!</p>"
)
return
if self.NCBI_model.arraydata:
self.interrupt = False
self.progressDialog = self.factory.myProgressDialog(
"Please Wait", "Downloading...", parent=self)
self.progressDialog.show()
self.worker_download = WorkThread(self.downloadSeq, parent=self)
self.progressDialog.canceled.connect(lambda: [
setattr(self, "interrupt", True),
self.worker_download.stopWork(),
self.progressDialog.close()
])
self.worker_download.finished.connect(self.downloadDone)
self.worker_download.start()
else:
QMessageBox.information(
self, "Information",
"<p style='line-height:25px; height:25px'>Please search first!</p>"
)
def downloadSeq(self):
try:
checked_ids = self.NCBI_model.list_checked
# if not checked_ids:
# checked_ids = self.NCBI_model.fetchAllIDs()
batch_size = 20
count = len(checked_ids) if checked_ids else self.count
self.download_contents = ""
for start in range(0, count, batch_size):
if self.interrupt:
return
end = min(count, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > count:
batch_size = count - start
if not checked_ids:
#下载所有序列的模式
fetch_handle = Entrez.efetch(db=self.database,
rettype=self.rettype,
retmode="text",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
else:
fetch_handle = Entrez.efetch(db=self.database,
rettype=self.rettype,
retmode="text",
retstart=start,
retmax=batch_size,
id=checked_ids)
self.download_contents += fetch_handle.read()
self.progressDiologSig.emit(end * 100 / count)
# index = self.comboBox.currentIndex()
# filepath = self.comboBox.itemData(index, role=Qt.ToolTipRole)
# self.downloadFinished.emit()
except:
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
def downloadDone(self):
self.progressDialog.close()
QMessageBox.information(
self, "Download finished",
"<p style='line-height:25px; height:25px'>Done! Back to home page to view them.</p>"
)
if self.rettype == "gb":
self.inputContentSig.emit(self.download_contents, self.outputPath)
else:
with open(self.outputPath + os.sep + self.fasta_file_name,
"w",
encoding="utf-8") as f:
f.write(self.download_contents)
self.fastaDownloadFinishedSig.emit(self.outputPath)
def startSearch(self):
if hasattr(self, "worker") and self.worker.isRunning():
return
if self.spinBox.value() == 0:
self.spinBox.setValue(20)
if self.lineEdit.text():
self.interrupt = False
self.NCBI_model.init_table() #刷新一下table（归零）
self.worker = WorkThread(self.search, parent=self)
self.worker.start()
else:
QMessageBox.information(
self, "Search in NCBI",
"<p style='line-height:25px; height:25px'>Please input keywords first!</p>"
)
def guiSave(self):
# Save geometry
self.serhNCBI_settings.setValue('size', self.size())
# self.serhNCBI_settings.setValue('pos', self.pos())
for name, obj in inspect.getmembers(self):
# if type(obj) is QComboBox: # this works similar to isinstance, but
# missed some field... not sure why?
# if isinstance(obj, QComboBox):
# # save combobox selection to registry
# text = obj.currentText()
# if text:
# allItems = [
# obj.itemText(i) for i in range(obj.count())]
# allItems.remove(text)
# sortItems = [text] + allItems
# self.serhNCBI_settings.setValue(name, sortItems)
if isinstance(obj, QLineEdit):
if name == "lineEdit":
self.serhNCBI_settings.setValue(name, self.completer_texts)
if isinstance(obj, QSpinBox):
if name == "spinBox":
self.serhNCBI_settings.setValue(name, self.display_items)
def guiRestore(self):
# Restore geometry
self.resize(self.serhNCBI_settings.value('size', QSize(1000, 600)))
self.factory.centerWindow(self)
# self.move(self.serhNCBI_settings.value('pos', QPoint(875, 254)))
for name, obj in inspect.getmembers(self):
if isinstance(obj, QComboBox):
if name == "comboBox":
allItems = self.factory.fetchAllWorkFolders(self.workPath)
model = obj.model()
obj.clear()
for num, i in enumerate(allItems):
if self.parent.isWorkFolder(i, mode="gb"):
text = "\"%s\" in GenBank_File (GenBank format)" % os.path.basename(
i)
else:
text = "\"%s\" in Other_File (Fasta format)" % os.path.basename(
i)
item = QStandardItem(text)
item.setToolTip(i)
# 背景颜色
if num % 2 == 0:
item.setBackground(QColor(255, 255, 255))
else:
item.setBackground(QColor(237, 243, 254))
model.appendRow(item)
# obj.setCurrentText(os.path.basename(self.workPath))
if self.parent.isWorkFolder(self.workPath, mode="gb"):
obj.setCurrentText(
"\"%s\" in GenBank_File (GenBank format)" %
os.path.basename(self.workPath))
else:
obj.setCurrentText(
"\"%s\" in Other_File (Fasta format)" %
os.path.basename(self.workPath))
if isinstance(obj, QLineEdit):
if name == "lineEdit":
self.completer_texts = self.serhNCBI_settings.value(
name, []) # get stored value from registry
self.setLCompleter()
if isinstance(obj, QSpinBox):
if name == "spinBox":
self.display_items = int(
self.serhNCBI_settings.value(
name, 100)) # get stored value from registry
obj.setValue(self.display_items)
def runProgressDialog(self, num):
oldValue = self.progressDialog.value()
done_int = int(num)
if done_int > oldValue:
self.progressDialog.setProperty("value", done_int)
QCoreApplication.processEvents()
if done_int == 100:
self.progressDialog.close()
def popupException(self, exception):
if ("getaddrinfo failed" in exception) or ("RuntimeError"
in exception):
text = "<p style='line-height:25px; height:25px'>Search failed, try to check your network connection!</p>"
else:
text = "<p style='line-height:25px; height:25px'>The search failed for some of the sequences. As this may have been caused by a network problem, you can wait for a while and try again.<br> If the problem persists you may report it at " \
"<a href=\"https://github.com/dongzhang0725/PhyloSuite/issues\">https://github.com/dongzhang0725/PhyloSuite/issues</a> " \
"or send an email with the detailed traceback to [email protected]</p>"
msg = QMessageBox(self)
msg.setIcon(QMessageBox.Critical)
msg.setText(text)
msg.setWindowTitle("Error")
msg.setDetailedText(exception)
msg.setStandardButtons(QMessageBox.Ok)
msg.exec_()
def closeEvent(self, event):
self.interrupt = True
if hasattr(self, "worker") and self.worker.isRunning():
self.worker.stopWork()
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
self.worker_addition.stopWork()
if hasattr(self,
"worker_download") and self.worker_download.isRunning():
self.worker_download.stopWork()
if hasattr(self, "progressDialog"):
self.progressDialog.close()
self.guiSave()
# self.log_gui.close() # 关闭子窗口
def eventFilter(self, obj, event):
name = obj.objectName()
if event.type() == QEvent.KeyPress: # 首先得判断type
if event.key() == Qt.Key_Return:
if name == "lineEdit":
self.sync_completer_texts(self.lineEdit.text())
self.startSearch()
return True
if name == "spinBox":
self.on_toolButton_2_clicked()
return True
# return QMainWindow.eventFilter(self, obj, event) #
# 其他情况会返回系统默认的事件处理方法。
return super(SerhNCBI, self).eventFilter(obj, event) # 0
def sync_completer_texts(self, text):
if text and (text not in self.completer_texts):
self.completer_texts.insert(0, text)
if len(self.completer_texts) > 15:
self.completer_texts = self.completer_texts[:15]
self.guiSave()
self.setLCompleter()
def setLCompleter(self):
comp = QCompleter(self.completer_texts)
comp.setFilterMode(Qt.MatchContains)
comp.setCompletionMode(QCompleter.UnfilteredPopupCompletion)
# comp.popup().setStyleSheet("background-color: yellow")
self.lineEdit.setCompleter(comp)
def init_list(self):
self.list_table_header = [
"ID", "Description", "Organism", "Length", "Update date",
"Taxonomy", "Create date", "Molecular type", "Topology",
"References", "Source", "Keywords", "Project", "Other IDs",
"Strandedness", "Comments"
]
def updateTable(self, list_):
# print(array)
# 测试array是新添加的list
self.NCBI_model.appendTable(list_)
def ctrlSearchState(self, state):
if state == "searching":
self.disp_check_label.setText("Searching...")
self.disp_check_label.setVisible(True)
self.disp_check_gifLabel.setVisible(True)
self.lineEdit.buttonSearch.setDisabled(True)
self.lineEdit.buttonStop.setDisabled(False)
self.toolButton_2.setDisabled(True)
self.toolButton_3.setDisabled(True)
elif state == "fetching":
self.disp_check_label.setText("Fetching...")
self.disp_check_label.setVisible(True)
self.disp_check_gifLabel.setVisible(True)
self.disp_check_progress.setValue(0)
self.disp_check_progress.setVisible(True)
self.lineEdit.buttonStop.setDisabled(False)
elif state == "except":
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.buttonSearch.setDisabled(False)
self.lineEdit.buttonStop.setDisabled(True)
self.toolButton_2.setDisabled(False)
self.toolButton_3.setDisabled(False)
elif state == "finished":
self.disp_check_label.setVisible(False)
self.disp_check_gifLabel.setVisible(False)
self.disp_check_progress.setVisible(False)
self.lineEdit.buttonSearch.setDisabled(False)
self.lineEdit.buttonStop.setDisabled(True)
self.toolButton_2.setDisabled(False)
self.toolButton_3.setDisabled(False)
##如果啥也没搜到
self.exist_base = self.NCBI_model.rowCount(self.tableView)
if not self.exist_base:
QMessageBox.information(
self, "Download finished",
"<p style='line-height:25px; height:25px'>No items found!</p>"
)
def ctrlItems(self, count):
count = count if count != 0 else 20
self.spinBox.setMaximum(count)
if count == 0:
self.spinBox.setValue(20)
self.label_4.setText("items of %s (total)" % count)
self.label_2.setText("Download all (%s) sequences to:" % count)
# if count < self.display_items:
# self.display_items = count
# self.spinBox.setValue(count)
def searchProgress(self, value):
oldValue = self.disp_check_progress.value()
done_int = int(value)
if done_int > oldValue:
self.disp_check_progress.setProperty("value", done_int)
QCoreApplication.processEvents()
def sync_display_items(self, value):
self.display_items = value
def search(self):
try:
self.searchSig.emit("searching")
self.init_list()
self.ctrl_text() #文本还原
self.NCBI_model.list_checked = []
self.database = self.comboBox_2.currentText()
keywords = self.lineEdit.text()
email = self.lineEdit_2.text()
email = email if email else "*****@*****.**"
Entrez.email = email
search_handle = Entrez.esearch(db=self.database,
term=keywords,
usehistory="y")
search_results = Entrez.read(search_handle)
self.webenv = search_results["WebEnv"]
self.query_key = search_results["QueryKey"]
self.count = int(search_results["Count"])
self.ctrlItemsSig.emit(
self.count) #如果只有2个序列，self.display_items也会变成2
search_handle.close()
batch_size = 20
self.searchSig.emit("fetching")
# time_start = time.time()
total_displayed = self.display_items
if self.count < total_displayed:
total_displayed = self.count
for start in range(0, total_displayed, batch_size):
# try:
if self.interrupt:
return
end = min(total_displayed, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > total_displayed:
batch_size = total_displayed - start
fetch_handle = Entrez.efetch(db=self.database,
retmode="xml",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
fetch_records = Entrez.read(fetch_handle)
for num, record in enumerate(fetch_records):
list_ = []
for i in [
"GBSeq_accession-version", "GBSeq_definition",
"GBSeq_organism", "GBSeq_length",
"GBSeq_update-date", "GBSeq_taxonomy",
"GBSeq_create-date", "GBSeq_moltype",
"GBSeq_topology", "GBSeq_references",
"GBSeq_source", "GBSeq_keywords", "GBSeq_project",
"GBSeq_other-seqids", "GBSeq_strandedness",
"GBSeq_comment"
]:
if i in record:
list_.append(str(record[i]))
else:
list_.append("N/A")
self.updateSig.emit(list_)
self.progressBarSig.emit(
(start + num + 1) * 100 / total_displayed)
fetch_handle.close()
# except:
# pass
self.searchSig.emit("finished")
except:
self.searchSig.emit("except")
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
# time_end = time.time()
# print("time:", time_end - time_start)
def addition_search(self):
try:
total_displayed = self.display_items
if self.count < total_displayed:
total_displayed = self.count
batch_size = 20
self.searchSig.emit("fetching")
for start in range(self.exist_base, total_displayed, batch_size):
if self.interrupt:
break
end = min(total_displayed, start + batch_size)
print("Going to download record %i to %i" % (start + 1, end))
if (start + batch_size) > total_displayed:
batch_size = total_displayed - start
fetch_handle = Entrez.efetch(db=self.database,
retmode="xml",
retstart=start,
retmax=batch_size,
webenv=self.webenv,
query_key=self.query_key)
fetch_records = Entrez.read(fetch_handle)
for num, record in enumerate(fetch_records):
list_ = []
for i in [
"GBSeq_accession-version", "GBSeq_definition",
"GBSeq_organism", "GBSeq_length",
"GBSeq_update-date", "GBSeq_taxonomy",
"GBSeq_create-date", "GBSeq_moltype",
"GBSeq_topology", "GBSeq_references",
"GBSeq_source", "GBSeq_keywords", "GBSeq_project",
"GBSeq_other-seqids", "GBSeq_strandedness",
"GBSeq_comment"
]:
if i in record:
list_.append(str(record[i]))
else:
list_.append("N/A")
self.updateSig.emit(list_)
self.progressBarSig.emit(
(start - self.exist_base + num + 1) * 100 /
(total_displayed - self.exist_base))
# self.progressBarSig.emit((start - self.exist_base)*100/(total_displayed - self.exist_base))
fetch_handle.close()
self.searchSig.emit("finished")
except:
self.searchSig.emit("except")
self.exception_signal.emit(''.join(
traceback.format_exception(*sys.exc_info())))
def ctrl_text(self):
selected_num = len(self.NCBI_model.list_checked)
if selected_num:
self.label_2.setText("Download selected (%d) sequences to:" %
(selected_num))
else:
text = "Download all (%d) sequences to:" % self.count if hasattr(
self, "count") else "Download all sequences to:"
self.label_2.setText(text)
def openID(self):
indices = self.tableView.selectedIndexes()
arraydata = self.NCBI_model.arraydata
ID = arraydata[indices[0].row()][0].text()
url = "https://www.ncbi.nlm.nih.gov/nuccore/%s"%ID if self.comboBox_2.currentText() == "nucleotide" \
else "https://www.ncbi.nlm.nih.gov/protein/%s"%ID
QDesktopServices.openUrl(QUrl(url))
def stopSearch(self):
self.interrupt = True
if hasattr(self, "worker") and self.worker.isRunning():
self.worker.stopWork()
if hasattr(self,
"worker_addition") and self.worker_addition.isRunning():
self.worker_addition.stopWork()
self.searchSig.emit("except")
def check_displayed(self, isCheck):
if hasattr(self, "NCBI_model") and self.NCBI_model.rowCount(
self.tableView):
# self.NCBI_model.beginResetModel()
self.NCBI_model.layoutAboutToBeChanged.emit()
if isCheck:
self.NCBI_model.list_checked = [
i[0].text() for i in self.NCBI_model.arraydata
]
else:
self.NCBI_model.list_checked = []
self.NCBI_model.layoutChanged.emit()
self.ctrl_text()
