class TimeJumpDialog(QDialog):
def __init__(self, parent: QWidget) -> None:
super().__init__(parent)
self.setWindowTitle("Select time...")
self._label = QLabel("", self)
self._time_edit = TimeEdit(self)
self._radio_rel = QRadioButton("Relative", self)
self._radio_abs = QRadioButton("Absolute", self)
if relative_checked:
self._radio_rel.setChecked(True)
else:
self._radio_abs.setChecked(True)
strip = QDialogButtonBox(self)
strip.addButton(strip.Ok)
strip.addButton(strip.Cancel)
if not show_radio:
self._radio_abs.setHidden(True)
self._radio_rel.setHidden(True)
strip.accepted.connect(self.accept)
strip.rejected.connect(self.reject)
self._radio_rel.clicked.connect(self._on_radio_click)
self._radio_abs.clicked.connect(self._on_radio_click)
layout = QVBoxLayout(self)
layout.addWidget(self._label)
layout.addWidget(self._time_edit)
layout.addWidget(self._radio_rel)
layout.addWidget(self._radio_abs)
layout.addWidget(strip)
self._on_radio_click()
self._time_edit.set_value(value)
def _on_radio_click(self) -> None:
is_relative = self._radio_rel.isChecked()
if is_relative:
self._label.setText(relative_label)
else:
self._label.setText(absolute_label)
self._time_edit.set_allow_negative(is_relative)
def value(self) -> tuple[int, bool]:
return (self._time_edit.get_value(), self._radio_rel.isChecked())
class App(QMainWindow):
def __init__(self, multithread: bool):
super().__init__()
self.title = "ProteoSushi"
self.left = 10
self.top = 10
self.width = 640
self.height = 480
self.multithread = multithread
self.centralWidget = QWidget()
self.setCentralWidget(self.centralWidget)
self.setWindowTitle("ProteoSushi")
self.setWindowIcon(QIcon("ProteoSushi_icon.png"))
self.species_id_dict = self.__make_species_dict()
self.species_name_dict = {
v: k
for k, v in self.species_id_dict.items()
}
self.threadpool = QThreadPool()
self.initUI()
def initUI(self):
self.setWindowTitle(self.title)
self.setGeometry(self.left, self.top, self.width, self.height)
self.file_chooser_label = QLabel("Types of ProteoSushi Files", self)
self.maxquant_RB = QRadioButton("MaxQuant", self)
self.maxquant_RB.toggled.connect(self.check_MQ_RB)
self.maxquant_RB.setToolTip(
"Use the txt output folder from the MaxQuant Search Engine")
self.maxquant_button = QPushButton("MaxQuant txt Folder")
self.maxquant_button.setHidden(True)
self.maxquant_button.clicked.connect(self.onClickMQbutton)
self.maxquant_filepath = QLabel("[Filepath]", self)
self.maxquant_filepath.setHidden(True)
self.mascot_RB = QRadioButton("Mascot", self)
self.mascot_RB.toggled.connect(self.check_mascot_RB)
self.mascot_RB.setToolTip(
"Use the output from the Mascot Search Engine")
self.mascot_button = QPushButton("Mascot File")
self.mascot_button.setHidden(True)
self.mascot_button.clicked.connect(self.onClickMascotButton)
self.mascot_filepath = QLabel("[Filepath]", self)
self.mascot_filepath.setHidden(True)
self.generic_RB = QRadioButton("Generic", self)
self.generic_RB.toggled.connect(self.check_generic_RB)
self.generic_RB.setToolTip(
"Use the output from any other search engine")
self.generic_button = QPushButton("Generic File")
self.generic_button.setHidden(True)
self.generic_button.clicked.connect(self.onClickGenericButton)
self.generic_filepath = QLabel("[Filepath]", self)
self.generic_filepath.setHidden(True)
self.search_engine_group = QButtonGroup()
self.search_engine_group.addButton(self.maxquant_RB)
self.search_engine_group.addButton(self.mascot_RB)
self.search_engine_group.addButton(self.generic_RB)
self.PTM_CBs = list()
self.proteome_filepath_button = QPushButton("Uniprot Proteome FASTA")
self.proteome_filepath_button.clicked.connect(
self.on_click_proteome_button)
self.proteome_filepath = QLabel("[Filepath]", self)
self.output_filepath_button = QPushButton("Output Name and Location")
self.output_filepath_button.clicked.connect(
self.on_click_output_button)
self.output_filepath = QLabel("[Filepath]", self)
self.options_label = QLabel("Options", self)
self.localization_checkbox = QCheckBox("Localization Threshold", self)
self.localization_checkbox.stateChanged.connect(
self.check_localization_checkbox)
self.localization_checkbox.setHidden(True)
self.localization_checkbox.setToolTip(
"Set a threshold for the localization probability for all PTM sites"
)
self.localization_edit = QLineEdit(self)
self.localization_edit.setHidden(True)
self.localization_edit.setToolTip(
"Set a threshold for the localization probability for all PTM sites"
)
self.target_checkbox = QCheckBox("Use Target Genes", self)
self.target_checkbox.stateChanged.connect(self.checkTargetBox)
self.target_checkbox.setToolTip(
"Use a list of genes that will be prioritized given multiple matches"
)
self.target_button = QPushButton("Target Gene List")
self.target_button.setHidden(True)
self.target_button.clicked.connect(self.onClickTargetButton)
self.target_filepath = QLabel("[Filepath]", self)
self.target_filepath.setHidden(True)
self.quant_CB = QCheckBox("Use Quantitation Values", self)
self.quant_CB.stateChanged.connect(self.check_quant_CB)
self.quant_CB.setToolTip(
"Whether to use the Intensity/Quantitation values from the PSMs")
self.sum_RB = QRadioButton("Sum Peaks", self)
self.sum_RB.setHidden(True)
self.average_RB = QRadioButton("Average Peaks", self)
self.average_RB.setHidden(True)
self.quant_method_group = QButtonGroup()
self.quant_method_group.addButton(self.sum_RB)
self.quant_method_group.addButton(self.average_RB)
self.uniprot_annot_CB = QCheckBox("Annotate with Uniprot", self)
self.uniprot_annot_CB.setToolTip(
"Whether to add in annotation from Uniprot, like subcellular location, secondary structure, etc."
)
self.species_id_label = QLabel("Species ID", self)
self.species_id_label.setToolTip(
"The species ID for the species from the data provided (e.g. 9606)"
)
self.species_id_edit = QLineEdit(self)
self.species_id_edit.editingFinished.connect(self.update_species_name)
self.species_id_edit.setToolTip(
"The species ID for the species from the data provided (e.g. 9606)"
)
self.species_name_label = QLabel("", self)
self.max_missed_label = QLabel("Max Missed Cleavages", self)
self.max_missed_label.setToolTip(
"The maximum allowed missed cleavages for a given peptide")
self.max_missed_edit = QLineEdit(self)
self.max_missed_edit.setToolTip(
"The maximum allowed missed cleavages for a given peptide")
self.fdr_CB = QCheckBox("FDR Threshold", self)
self.fdr_CB.stateChanged.connect(self.check_fdr_CB)
self.fdr_CB.setToolTip(
"[OPTIONAL] The threshold for pep_expect column for Mascot or PEP column for Maxquant.\nMust be between 0 and 1, but can be left blank."
)
self.fdr_edit = QLineEdit(self) # TODO: Error check for a number
self.fdr_edit.setHidden(True)
self.fdr_edit.setToolTip(
"[OPTIONAL] The threshold for pep_expect column for Mascot or PEP column for Maxquant.\nMust be between 0 and 1, but can be left blank."
)
self.protease_label = QLabel("Protease used in sample digestion", self)
self.protease_label.setToolTip(
"The protease used to digest the sample\nExamples include: trypsin/p, trypsin!p, lys-c, asp-n, asp-ne, lys-n"
)
self.protease_combo_box = QComboBox()
self.protease_combo_box.setToolTip(
"The protease used to digest the sample\nExamples include: trypsin/p, trypsin!p, lys-c, asp-n, asp-ne, lys-n"
)
self.protease_combo_box.addItems(
["trypsin/p", "trypsin!p", "lys-c", "asp-n", "asp-ne", "lys-n"])
self.protease_combo_box.setEditable(True)
self.run_button = QPushButton("Rollup!")
self.run_button.setHidden(False)
self.run_button.clicked.connect(self.onClickRunButton)
self.createGridLayout()
windowLayout = QVBoxLayout(self.centralWidget)
windowLayout.addWidget(self.horizontalGroupBox)
windowLayout.setAlignment(Qt.AlignTop)
self.setLayout(windowLayout)
self.show()
def check_MQ_RB(self, state):
if self.maxquant_RB.isChecked():
self.maxquant_filepath.setHidden(False)
self.maxquant_button.setHidden(False)
self.localization_checkbox.setHidden(False)
if self.localization_checkbox.isChecked():
self.localization_edit.setHidden(False)
else:
self.maxquant_filepath.setHidden(True)
self.maxquant_button.setHidden(True)
self.localization_checkbox.setHidden(True)
self.localization_edit.setHidden(True)
def check_mascot_RB(self, state):
if self.mascot_RB.isChecked():
self.mascot_filepath.setHidden(False)
self.mascot_button.setHidden(False)
else:
self.mascot_filepath.setHidden(True)
self.mascot_button.setHidden(True)
def check_generic_RB(self, state):
if self.generic_RB.isChecked():
self.generic_filepath.setHidden(False)
self.generic_button.setHidden(False)
self.localization_checkbox.setHidden(False)
if self.localization_checkbox.isChecked():
self.localization_edit.setHidden(False)
else:
self.generic_filepath.setHidden(True)
self.generic_button.setHidden(True)
self.localization_checkbox.setHidden(True)
self.localization_edit.setHidden(True)
def checkTargetBox(self, state):
if state == QtCore.Qt.Checked:
self.target_filepath.setHidden(False)
self.target_button.setHidden(False)
else:
self.target_filepath.setHidden(True)
self.target_button.setHidden(True)
def check_quant_CB(self, state):
if state == QtCore.Qt.Checked:
self.average_RB.setHidden(False)
self.sum_RB.setHidden(False)
else:
self.average_RB.setHidden(True)
self.sum_RB.setHidden(True)
def check_fdr_CB(self, state):
if state == QtCore.Qt.Checked:
self.fdr_edit.setHidden(False)
else:
self.fdr_edit.setHidden(True)
def check_localization_checkbox(self, state):
if state == QtCore.Qt.Checked and (self.maxquant_RB.isChecked()
or self.generic_RB.isChecked()):
self.localization_edit.setHidden(False)
else:
self.localization_edit.setHidden(True)
def update_species_name(self):
if not self.species_id_edit.text():
self.species_name_label.setStyleSheet("background-color : white")
self.species_name_label.setText("")
elif self.species_id_edit.text() in self.species_id_dict:
self.species_name_label.setStyleSheet("background-color : white")
self.species_name_label.setText(
self.species_id_dict[self.species_id_edit.text()][2:])
elif f"N={self.species_id_edit.text()}" in self.species_name_dict:
self.species_name_label.setStyleSheet("background-color : white")
self.species_name_label.setText(self.species_id_edit.text())
self.species_id_edit.setText(
self.species_name_dict[f"N={self.species_id_edit.text()}"])
else:
self.species_name_label.setText("Not a valid species ID")
self.species_name_label.setStyleSheet("background-color : red")
def checkRunButton(self, MQcheckState, MQfilepath: str, mascotCheckState,
mascot_filepath: str, genericCheckState,
generic_filepath: str):
"""Checks to see whether the run button is available. must have a search engine output and missed cleavages, etc
Arguments:
MQcheckState {QtCore.Qt.Checked} -- whether the box is checked
MQfilepath {str} -- the filepath for maxquant output
mascotCheckState {QtCore.Qt.Checked} -- whether the box is checked
mascot_filepath {str} -- the filepath for maxquant output
genericCheckState {QtCore.Qt.Checked} -- whether the box is checked
generic_filepath {str} -- the filepath for maxquant output
"""
# TODO: update to require species, etc.
if (((MQcheckState == QtCore.Qt.Checked and os.path.exists(MQfilepath))
or (mascotCheckState == QtCore.Qt.Checked
and os.path.exists(mascot_filepath)) or
(genericCheckState == QtCore.Qt.Checked
and os.path.exists(generic_filepath)))
and os.path.exists(self.proteome_filepath.text())):
self.run_button.setHidden(False)
else:
self.run_button.setHidden(True)
def __make_species_dict(self):
species_id_dict = dict()
with pkg_resources.open_text(lib, "spec_list_fixed.tsv") as spec_list:
#with pkg_resources.open_text(__package__, "spec_list_fixed.tsv") as spec_list:
for line in spec_list:
split_line = line.strip().split('\t')
species_id_dict[split_line[0]] = split_line[1]
return species_id_dict
def openCSVFileNameDialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, _ = QFileDialog.getOpenFileName(
self,
"Choose the Search Engine Output",
os.getcwd(),
"CSV Files (*.csv);;All Files (*)",
options=options)
return fileName
def openTXTFileNameDialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, _ = QFileDialog.getOpenFileName(
self,
"Choose the Gene Name File",
os.getcwd(),
"TXT Files (*.txt);;All Files (*)",
options=options)
return fileName
def open_directory_dialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
dir_name = str(
QFileDialog.getExistingDirectory(self,
"Select Directory",
os.getcwd(),
options=options))
return dir_name
def openFASTAFileNameDialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, _ = QFileDialog.getOpenFileName(
self,
"Choose the Proteome FASTA file",
os.getcwd(),
"FASTA Files (*.fasta);;All Files (*)",
options=options)
return fileName
def write_output_dialog(self):
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
fileName, _ = QFileDialog.getSaveFileName(
self,
"Choose the name and location of the output",
os.getcwd(),
"CSV Files (*.csv);;All Files (*)",
options=options)
return fileName
def convert_PTM_list(self, PTM_CBs: list) -> list:
"""changes the list of checkboxes into chosen ptms for analysis
Arguments:
PTM_CBs {list} -- a list of QCheckBoxes for each possible PTM
Returns:
list -- a list of strings of PTM names for analysis
"""
PTM_str_list = list()
for ptm_cb in PTM_CBs:
if ptm_cb.isChecked():
PTM_str_list.append(ptm_cb.text())
return PTM_str_list
@pyqtSlot()
def onClickMQbutton(self):
self.statusBar().showMessage("Choose the MaxQuant output FOLDER")
self.statusBar().setStyleSheet("background-color : white")
filename = self.open_directory_dialog()
#if self.maxquant_filepath.text() != "":
if os.path.exists(filename):
self.maxquant_filepath.setText(filename)
missed_cleavages, protease, PTMs = parse_output(
"maxquant", filename)
self.max_missed_edit.setText(str(missed_cleavages))
self.protease_combo_box.setEditText(protease)
#Remove the previous PTM checkboxes (if there were any)
if self.PTM_CBs != []:
for cb in self.PTM_CBs:
self.layout.removeWidget(cb)
cb.deleteLater()
# Adds the new checkboxes to the list
self.PTM_CBs = []
for ptm in PTMs:
self.PTM_CBs.append(QCheckBox(ptm, self))
# Removes the label
i = 0
if not self.layout.itemAtPosition(5, i) is None:
label_to_remove = self.layout.itemAtPosition(5, i).widget()
self.layout.removeWidget(label_to_remove)
label_to_remove.deleteLater()
# Inserts the new PTM checkboxes
self.layout.addWidget(QLabel("PTMs for Current Analysis"), 5, i)
for widget in self.PTM_CBs:
self.layout.addWidget(widget, 6, i)
i += 1
self.statusBar().showMessage("")
@pyqtSlot()
def onClickMascotButton(self):
self.statusBar().showMessage("Choose the Mascot output file")
self.statusBar().setStyleSheet("background-color : white")
filename = self.openCSVFileNameDialog()
#if self.mascot_filepath.text() != "":
if os.path.exists(filename):
self.mascot_filepath.setText(filename)
missed_cleavages, protease, PTMs = parse_output("mascot", filename)
if missed_cleavages == -5:
self.statusBar().showMessage("Invalid Mascot file")
self.statusBar().setStyleSheet("background-color : red")
self.mascot_filepath.setText("")
return
self.max_missed_edit.setText(str(missed_cleavages))
self.protease_combo_box.setEditText(protease)
#Remove the previous PTM checkboxes (if there were any)
if self.PTM_CBs != []:
for cb in self.PTM_CBs:
self.layout.removeWidget(cb)
cb.deleteLater()
# Adds the new checkboxes to the list
self.PTM_CBs = []
for ptm in PTMs:
self.PTM_CBs.append(QCheckBox(ptm, self))
# Removes the label
i = 0
if not self.layout.itemAtPosition(5, i) is None:
label_to_remove = self.layout.itemAtPosition(5, i).widget()
self.layout.removeWidget(label_to_remove)
label_to_remove.deleteLater()
# Inserts the new PTM checkboxes
self.layout.addWidget(QLabel("PTMs for Current Analysis"), 5, i)
for widget in self.PTM_CBs:
self.layout.addWidget(widget, 6, i)
i += 1
self.statusBar().showMessage("")
@pyqtSlot()
def onClickGenericButton(self):
self.statusBar().showMessage("Choose the Search Engine output")
self.statusBar().setStyleSheet("background-color : white")
filename = self.openCSVFileNameDialog()
#if self.generic_filepath.text() != "":
if os.path.exists(filename):
self.generic_filepath.setText(filename)
missed_cleavages, protease, PTMs = parse_output(
"generic", filename)
if missed_cleavages == -3:
self.statusBar().showMessage(
"A sequence in the Peptide Modified Sequence column is missing PTMs"
)
self.statusBar().setStyleSheet("background-color : red")
return
if missed_cleavages == -4:
self.statusBar().showMessage("Invalid file")
self.statusBar().setStyleSheet("background-color : red")
self.generic_filepath.setText("")
return
#Remove the previous PTM checkboxes (if there were any)
if self.PTM_CBs != []:
for cb in self.PTM_CBs:
self.layout.removeWidget(cb)
cb.deleteLater()
# Adds the new checkboxes to the list
self.PTM_CBs = []
for ptm in PTMs:
self.PTM_CBs.append(QCheckBox(ptm, self))
# Removes the label# This is where the MQ localization probability threshold will be
i = 0
if not self.layout.itemAtPosition(5, i) is None:
label_to_remove = self.layout.itemAtPosition(5, i).widget()
self.layout.removeWidget(label_to_remove)
label_to_remove.deleteLater()
# Inserts the new PTM checkboxes
self.layout.addWidget(QLabel("PTMs for Current Analysis"), 5, i)
for widget in self.PTM_CBs:
self.layout.addWidget(widget, 6, i)
i += 1
self.statusBar().showMessage("")
@pyqtSlot()
def on_click_proteome_button(self):
self.statusBar().showMessage("Choose the Uniprot Proteome FASTA file")
self.statusBar().setStyleSheet("background-color : white")
filename = self.openFASTAFileNameDialog()
if os.path.exists(filename):
# Parse the file to check it is valid and grab the species
was_error, species_ID = parse_proteome(filename)
if was_error:
self.statusBar().showMessage(
"ERROR: Invalid proteome FASTA file!")
self.statusBar().setStyleSheet("background-color : red")
else:
self.proteome_filepath.setText(filename)
if not species_ID is None:
self.species_id_edit.setText(species_ID)
self.update_species_name()
self.statusBar().showMessage("")
@pyqtSlot()
def on_click_output_button(self):
self.statusBar().showMessage(
"Choose the ProteoSushi output file location")
self.statusBar().setStyleSheet("background-color : white")
filename = self.write_output_dialog()
self.output_filepath.setText(filename)
self.statusBar().showMessage("")
@pyqtSlot()
def onClickTargetButton(self):
self.statusBar().showMessage("Choose the Target Gene file")
self.statusBar().setStyleSheet("background-color : white")
filename = self.openTXTFileNameDialog()
if self.target_filepath.text() != "":
self.target_filepath.setText(filename)
self.statusBar().showMessage("")
def __run_single_thread(self, fdr: float, combine_method, species_id,
localization: float):
"""Runs the background on the same thread if there are problems"""
# If the maxquant option was chosen, it sends that info to be run
if self.maxquant_RB.isChecked() and os.path.exists(
self.maxquant_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"maxquant",
self.maxquant_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
localization)
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and output == 502:
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
elif self.mascot_RB.isChecked() and os.path.exists(
self.mascot_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"mascot",
self.mascot_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
None)
# If the mascot file has no intensity values and user tried to analyze them
if self.quant_CB.isChecked() and output == 2:
self.statusBar().showMessage(
"ERROR: Mascot file has no detectable intensity values!")
self.statusBar().setStyleSheet("background-color : red")
return
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and output == 502:
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
elif self.generic_RB.isChecked() and os.path.exists(
self.generic_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"generic",
self.generic_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
localization)
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and (output == 502
or output == 4):
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
# If the generic file has no intensity values and user tried to analyze them
if self.quant_CB.isChecked() and output == 2:
self.statusBar().showMessage(
"ERROR: Generic file has no detectable intensity values!")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
else:
self.statusBar().showMessage(
"ERROR: Missing Search Engine Output!")
self.statusBar().setStyleSheet("background-color : red")
def __run_async(self, fdr: float, combine_method, species_id,
localization: float):
"""Function that runs the backend on a separate thread"""
# If the maxquant option was chosen, it sends that info to be run
if self.maxquant_RB.isChecked() and os.path.exists(
self.maxquant_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"maxquant",
self.maxquant_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
localization)
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and output == 502:
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
elif self.mascot_RB.isChecked() and os.path.exists(
self.mascot_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"mascot",
self.mascot_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
None)
# If the mascot file has no intensity values and user tried to analyze them
if self.quant_CB.isChecked() and output == 2:
self.statusBar().showMessage(
"ERROR: Mascot file has no detectable intensity values!")
self.statusBar().setStyleSheet("background-color : red")
return
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and output == 502:
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
elif self.generic_RB.isChecked() and os.path.exists(
self.generic_filepath.text()):
start_time = time()
self.statusBar().showMessage("Analysis in Progress")
self.statusBar().setStyleSheet("background-color : white")
output = rollup(
"generic",
self.generic_filepath.text(),
self.target_checkbox.isChecked(
), # Whether target will be used
self.target_filepath.text(),
int(self.max_missed_edit.text()),
self.protease_combo_box.currentText(),
fdr,
self.quant_CB.isChecked(),
self.convert_PTM_list(self.PTM_CBs),
self.proteome_filepath.text(),
combine_method,
self.uniprot_annot_CB.isChecked(),
species_id,
self.output_filepath.text(),
localization)
# If there is a 502 proxy error (server side error)
if self.uniprot_annot_CB.isChecked() and (output == 502
or output == 4):
self.statusBar().showMessage(
"ERROR: Uniprot server error! Please try again later.")
self.statusBar().setStyleSheet("background-color : red")
return
# If the generic file has no intensity values and user tried to analyze them
if self.quant_CB.isChecked() and output == 2:
self.statusBar().showMessage(
"ERROR: Generic file has no detectable intensity values!")
self.statusBar().setStyleSheet("background-color : red")
return
self.statusBar().showMessage("Analysis Complete!")
self.statusBar().setStyleSheet("background-color : green")
print("\033[92m {}\033[00m".format("\nAnalysis Complete!"))
print("\033[96m {}\033[00m".format(
f"Rollup took {time() - start_time} seconds"))
#sys.exit()
else:
self.statusBar().showMessage(
"ERROR: Missing Search Engine Output!")
self.statusBar().setStyleSheet("background-color : red")
#sys.exit()
def __cut_thread(self):
"""Called once the backend thread finishes"""
# Enables the buttons again in case I get multiple analyses working
self.run_button.setEnabled(True)
self.proteome_filepath_button.setEnabled(True)
self.output_filepath_button.setEnabled(True)
self.maxquant_button.setEnabled(True)
self.mascot_button.setEnabled(True)
self.generic_button.setEnabled(True)
#sys.exit()
return
@pyqtSlot()
def onClickRunButton(self):
if ((self.maxquant_RB.isChecked()
and os.path.exists(self.maxquant_filepath.text()))
or (self.mascot_RB.isChecked()
and os.path.exists(self.mascot_filepath.text()))
or (self.generic_RB.isChecked()
and os.path.exists(self.generic_filepath.text()))):
if not os.path.exists(self.proteome_filepath.text()):
self.statusBar().showMessage(
"ERROR: Missing Proteome FASTA file!")
self.statusBar().setStyleSheet("background-color : red")
return
# If the user didn't choose a name or location for the file
if self.output_filepath.text() == "":
self.statusBar().showMessage(
"ERROR: ProteoSushi output name and location not chosen!")
self.statusBar().setStyleSheet("background-color : red")
return
if os.path.isdir(self.output_filepath.text()):
self.output_filepath.setText(
os.path.join(self.output_filepath.text(),
"proteosushi_output.csv"))
if self.output_filepath.text() == "[Filepath]":
self.output_filepath.setText(
os.path.join(os.getcwd(), "proteosushi_output.csv"))
if self.output_filepath.text()[-4:] != ".csv":
self.output_filepath.setText(self.output_filepath.text() +
".csv")
try: # Check to see if the provided number of allowed missed cleavages is legal
max_missed = int(self.max_missed_edit.text())
if max_missed < 0:
self.statusBar().showMessage(
"ERROR: Number of max allowed missed cleavages cannot be less than 0!"
)
self.statusBar().setStyleSheet("background-color : red")
return
except ValueError:
self.statusBar().showMessage(
"ERROR: Invalid number for max allowed missed cleavages!")
self.statusBar().setStyleSheet("background-color : red")
return
# Checks that the localization prob threshold is between 0 and 1
try:
if self.localization_edit.text() != "":
localization = float(self.localization_edit.text())
if localization < 0 or localization > 1:
self.statusBar().showMessage(
"ERROR: Localization threshold must be between 0 and 1!"
)
self.statusBar().setStyleSheet(
"background-color : red")
return
else:
localization = None
except ValueError:
self.statusBar().showMessage(
"ERROR: Localization threshold must be a number between 0 and 1!"
)
self.statusBar().setStyleSheet("background-color : red")
return
try: # Checks to see if the provided FDR threshold is legal
if self.fdr_edit.text() != "":
fdr = float(self.fdr_edit.text())
if fdr < 0 or fdr > 1:
self.statusBar().showMessage(
"ERROR: FDR must be between 0 and 1!")
self.statusBar().setStyleSheet(
"background-color : red")
return
else:
fdr = None
except ValueError:
self.statusBar().showMessage("ERROR: FDR must be a number")
self.statusBar().setStyleSheet("background-color : red")
return
# If quantitation will be used, but the user has not selected a method to combine
if self.quant_CB.isChecked() and not self.sum_RB.isChecked(
) and not self.average_RB.isChecked():
self.statusBar().showMessage(
"ERROR: Must choose either Sum or Average for the quant method!"
)
self.statusBar().setStyleSheet("background-color : red")
return
elif self.quant_CB.isChecked() and self.sum_RB.isChecked():
combine_method = "sum"
elif self.quant_CB.isChecked() and self.average_RB.isChecked():
combine_method = "average"
else:
combine_method = ""
# If a valid species ID has been entered in
species_id = self.species_id_edit.text()
if len(species_id) > 0 and not species_id in self.species_id_dict:
self.statusBar().showMessage("ERROR: Not a valid species ID!")
self.statusBar().setStyleSheet("background-color : red")
return
if self.protease_combo_box.currentText() in cleave_rules:
# Disable all buttons before running to keep analysis confined
self.run_button.setEnabled(False)
self.proteome_filepath_button.setEnabled(False)
self.output_filepath_button.setEnabled(False)
self.maxquant_button.setEnabled(False)
self.mascot_button.setEnabled(False)
self.generic_button.setEnabled(False)
if not self.multithread:
self.__run_single_thread(fdr, combine_method, species_id,
localization)
else:
# Starts a new thread for the backend analysis; causes seg fault currently
print("\033[96m {}\033[00m".format("\nAnalysis Started!"))
worker = Worker(self.__run_async, fdr, combine_method,
species_id, localization)
worker.signals.end.connect(self.__cut_thread)
self.threadpool.start(worker)
else:
self.statusBar().showMessage(
"ERROR: Protease provided is not supported!")
self.statusBar().setStyleSheet("background-color : red")
else:
self.statusBar().showMessage(
"ERROR: Missing Search Engine Output!")
self.statusBar().setStyleSheet("background-color : red")
def createGridLayout(self):
self.horizontalGroupBox = QGroupBox("")
self.layout = QGridLayout()
self.layout.setRowStretch(0, 1)
self.layout.setRowStretch(9, 1)
row = 1
self.layout.addWidget(self.file_chooser_label, row, 0)
row += 1
self.layout.addWidget(self.maxquant_RB, row, 0)
self.layout.addWidget(self.maxquant_button, row, 1)
self.layout.addWidget(self.maxquant_filepath, row, 2)
row += 1
self.layout.addWidget(self.mascot_RB, row, 0)
self.layout.addWidget(self.mascot_button, row, 1)
self.layout.addWidget(self.mascot_filepath, row, 2)
row += 1
self.layout.addWidget(self.generic_RB, row, 0)
self.layout.addWidget(self.generic_button, row, 1)
self.layout.addWidget(self.generic_filepath, row, 2)
row += 1
# This is where the PTM label goes
row += 1
# This is where the PTM checkboxes go
row += 1
self.layout.addWidget(QLabel("Proteome File", self), row, 0)
self.layout.addWidget(self.proteome_filepath_button, row, 1)
self.layout.addWidget(self.proteome_filepath, row, 2)
row += 1
self.layout.addWidget(self.species_id_label, row, 0)
self.layout.addWidget(self.species_id_edit, row, 1)
self.layout.addWidget(self.species_name_label, row, 2)
row += 1
self.layout.addWidget(self.max_missed_label, row, 0)
self.layout.addWidget(self.max_missed_edit, row, 1)
row += 1
self.layout.addWidget(self.protease_label, row, 0)
self.layout.addWidget(self.protease_combo_box, row, 1)
row += 1
self.layout.addWidget(QLabel("Output Name & Location", self), row, 0)
self.layout.addWidget(self.output_filepath_button, row, 1)
self.layout.addWidget(self.output_filepath, row, 2)
row += 1
self.layout.addWidget(self.options_label, row, 0)
row += 1
self.layout.addWidget(self.localization_checkbox, row, 0)
self.layout.addWidget(self.localization_edit, row, 1)
row += 1
self.layout.addWidget(self.target_checkbox, row, 0)
self.layout.addWidget(self.target_button, row, 1)
self.layout.addWidget(self.target_filepath, row, 2)
row += 1
self.layout.addWidget(self.quant_CB, row, 0)
self.layout.addWidget(self.sum_RB, row, 1)
self.layout.addWidget(self.average_RB, row, 2)
row += 1
self.layout.addWidget(self.uniprot_annot_CB, row, 0)
row += 1
self.layout.addWidget(self.fdr_CB, row, 0)
self.layout.addWidget(self.fdr_edit, row, 1)
row += 1
self.layout.addWidget(self.run_button, row, 0)
self.layout.setAlignment(Qt.AlignTop)
self.horizontalGroupBox.setAlignment(Qt.AlignTop)
self.horizontalGroupBox.setLayout(self.layout)
