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gui.py
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from PyQt5 import QtWidgets
from PyQt5.QtCore import Qt, QObject, QThread, pyqtSignal # https://realpython.com/python-pyqt-qthread/
import sys
# mock matplotlib imports
sys.modules['matplotlib'] = __import__('matplotlib_mock')
import os
import logging
from logging.handlers import QueueListener
import time
import datetime
import multiprocessing
import mokapot
import numpy as np
from joblib import parallel_backend
import picked_group_fdr.pipeline.andromeda2pin as andromeda2pin
import picked_group_fdr.pipeline.update_evidence_from_pout as update_evidence
import picked_group_fdr.pipeline.merge_pout as merge_pout
import picked_group_fdr.picked_group_fdr as picked_group_fdr
import picked_group_fdr.utils.multiprocessing_pool as pool
import picked_group_fdr.digest as digest
logger = logging.getLogger()
logger.setLevel(logging.INFO)
def run_picked_group_fdr_all(evidence_files, pout_files, fasta_file, output_dir, digest_params, input_type):
try:
if len(output_dir) == 0:
raise RuntimeError("Please specify an output folder")
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if input_type == "rescoring":
run_update_evidence_rescoring(evidence_files, pout_files, output_dir)
run_picked_group_fdr(output_dir, fasta_file, digest_params)
elif input_type == "percolator":
run_merge_pout(pout_files, fasta_file, output_dir, digest_params)
run_picked_group_fdr_percolator_input(output_dir, fasta_file)
else:
run_andromeda_to_pin(evidence_files, fasta_file, output_dir, digest_params)
run_mokapot(output_dir)
run_update_evidence(evidence_files, output_dir)
run_picked_group_fdr(output_dir, fasta_file, digest_params)
except SystemExit as e:
logger.error(f"Error while running Picked Group FDR, exited with error code: {e}.")
except Exception as e:
logger.error(f"Error while running Picked Group FDR: {e}")
def run_andromeda_to_pin(evidence_files, fasta_file, output_dir, digest_params):
andromeda2pin.main(evidence_files + ['--outputTab', f'{output_dir}/pin.tab', '--databases', fasta_file] + digest_params)
def run_mokapot(output_dir):
np.random.seed(0) # TODO: Make seed configurable
psms = mokapot.read_pin(f'{output_dir}/pin.tab')
with parallel_backend("threading"):
results, models = mokapot.brew(psms)
results.to_txt(dest_dir=output_dir, decoys = True)
def run_update_evidence(evidence_files, output_dir):
update_evidence.main(
['--mq_evidence'] + evidence_files +
['--perc_results', f'{output_dir}/mokapot.psms.txt', f'{output_dir}/mokapot.decoys.psms.txt',
'--mq_evidence_out', f'{output_dir}/evidence_percolator.txt'])
def run_update_evidence_rescoring(evidence_files, pout_files, output_dir):
update_evidence.main(
['--mq_evidence'] + evidence_files +
['--perc_results'] + pout_files +
['--mq_evidence_out', f'{output_dir}/evidence_percolator.txt',
'--pout_input_type', 'prosit'])
def run_picked_group_fdr(output_dir, fasta_file, digest_params):
picked_group_fdr.main(
['--mq_evidence', f'{output_dir}/evidence_percolator.txt',
'--methods', 'picked_protein_group_mq_input',
'--do_quant',
'--protein_groups_out', f'{output_dir}/proteinGroups_percolator.txt',
'--fasta', fasta_file] + digest_params)
def run_merge_pout(pout_files, fasta_file, output_dir, digest_params):
merge_pout.main(
['--perc_results'] + pout_files +
['--perc_merged', f'{output_dir}/pout_merged.txt',
'--fasta', fasta_file] + digest_params)
def run_picked_group_fdr_percolator_input(output_dir, fasta_file):
picked_group_fdr.main(
['--perc_evidence', f'{output_dir}/pout_merged.txt',
'--methods', 'picked_protein_group_no_remap',
'--protein_groups_out', f'{output_dir}/proteinGroups_percolator.txt',
'--fasta', fasta_file])
# https://stackoverflow.com/questions/28655198/best-way-to-display-logs-in-pyqt#60528393
class QTextEditLogger(logging.Handler, QObject):
appendPlainText = pyqtSignal(str)
def __init__(self, parent):
super().__init__()
formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
formatter.converter = time.gmtime
self.setFormatter(formatter)
QObject.__init__(self)
self.widget = QtWidgets.QPlainTextEdit(parent)
self.widget.setReadOnly(True)
self.appendPlainText.connect(self.widget.appendPlainText)
def emit(self, record):
self.appendPlainText.emit(self.format(record))
# https://stackoverflow.com/questions/53288877/python-multiprocessing-sending-child-process-logging-to-gui-running-in-parent
class LogEmitter(QObject):
sigLog = pyqtSignal(str)
class LogHandler(logging.Handler):
def __init__(self):
super().__init__()
formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s")
formatter.converter = time.gmtime
self.setFormatter(formatter)
self.emitter = LogEmitter()
def emit(self, record):
msg = self.format(record)
self.emitter.sigLog.emit(msg)
class FileSelect(QtWidgets.QWidget):
def __init__(self, file_type, file_extensions, file_hint='', folder_select=False, *args, **kwargs):
super().__init__(*args, **kwargs)
self.file_type = file_type
self.file_hint = file_hint
self.file_extensions = file_extensions
self.label_text = f"Select {self.file_type} file"
if folder_select:
self.label_text = f"Select {self.file_type} folder"
self.file_hint_text = ""
if len(file_hint) > 0:
self.file_hint_text = f'<br><font color="grey">{self.file_hint}</font>'
self.label = QtWidgets.QLabel(self.label_text + self.file_hint_text)
self.hbox_layout = QtWidgets.QHBoxLayout()
self.hbox_layout.setContentsMargins(0, 0, 0, 0)
self.line_edit = QtWidgets.QLineEdit()
self.browse_button = QtWidgets.QPushButton("Browse")
if folder_select:
self.browse_button.clicked.connect(self.select_dir)
else:
self.browse_button.clicked.connect(self.select_file)
self.hbox_layout.addWidget(self.line_edit, stretch = 1)
self.hbox_layout.addWidget(self.browse_button)
self.setLayout(self.hbox_layout)
def select_file(self):
filename, _ = QtWidgets.QFileDialog.getOpenFileName(self, self.label_text, '', self.file_extensions)
self.line_edit.setText(filename)
def select_dir(self):
output_dir = QtWidgets.QFileDialog.getExistingDirectory(self, self.label_text , '', QtWidgets.QFileDialog.ShowDirsOnly)
self.line_edit.setText(output_dir)
def get_file(self):
return self.line_edit.text()
def setButtonsEnabled(self, enable):
self.browse_button.setEnabled(enable)
class MultiFileSelect(QtWidgets.QWidget):
def __init__(self, file_type, file_extensions, file_hint='', *args, **kwargs):
super().__init__(*args, **kwargs)
self.file_type = file_type
self.file_hint = file_hint
self.file_extensions = file_extensions
self.label_text = f"Select {self.file_type} file(s)"
self.file_hint_text = ""
if len(file_hint) > 0:
self.file_hint_text = f'<br><font color="grey">{self.file_hint}</font>'
self.label = QtWidgets.QLabel(self.label_text + self.file_hint_text)
self.hbox_layout = QtWidgets.QHBoxLayout()
self.hbox_layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.hbox_layout)
self.line_edit = QtWidgets.QListWidget()
self.line_edit.setSelectionMode(QtWidgets.QAbstractItemView.ExtendedSelection)
self.vbox_layout = QtWidgets.QVBoxLayout()
self.vbox_layout.setContentsMargins(0, 0, 0, 0)
self.vbox_layout.setAlignment(Qt.AlignTop)
self.browse_button = QtWidgets.QPushButton("Add")
self.browse_button.clicked.connect(self.add_files)
self.remove_button = QtWidgets.QPushButton("Remove")
self.remove_button.clicked.connect(self.remove_files)
self.vbox_layout.addWidget(self.browse_button)
self.vbox_layout.addWidget(self.remove_button)
self.hbox_layout.addWidget(self.line_edit, stretch = 1)
self.hbox_layout.addLayout(self.vbox_layout)
def add_files(self):
filenames, _ = QtWidgets.QFileDialog.getOpenFileNames(self, self.label_text, '', self.file_extensions)
self.line_edit.addItems(filenames)
def remove_files(self):
selected_items = self.line_edit.selectedItems()
if not selected_items:
return
for item in selected_items:
self.line_edit.takeItem(self.line_edit.row(item))
def get_files(self):
return [str(self.line_edit.item(i).text()) for i in range(self.line_edit.count())]
def setButtonsEnabled(self, enable):
self.browse_button.setEnabled(enable)
self.remove_button.setEnabled(enable)
class DigestionParametersGroup(QtWidgets.QGroupBox):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.digestion_group_layout = QtWidgets.QGridLayout()
self.setLayout(self.digestion_group_layout)
self.min_length_label = QtWidgets.QLabel("Min peptide length")
self.min_length_spinbox = QtWidgets.QSpinBox()
self.min_length_spinbox.setValue(digest.MIN_PEPLEN_DEFAULT)
self.min_length_spinbox.setRange(1,20)
self.max_length_label = QtWidgets.QLabel("Max peptide length")
self.max_length_spinbox = QtWidgets.QSpinBox()
self.max_length_spinbox.setValue(digest.MAX_PEPLEN_DEFAULT)
self.max_length_spinbox.setRange(1,100)
self.max_cleavages_label = QtWidgets.QLabel("Max miscleavages")
self.max_cleavages_spinbox = QtWidgets.QSpinBox()
self.max_cleavages_spinbox.setValue(digest.CLEAVAGES_DEFAULT)
self.max_cleavages_spinbox.setRange(1,10)
self.enzyme_label = QtWidgets.QLabel("Enzyme")
self.enzyme_select = QtWidgets.QComboBox()
self.enzyme_select.addItems(digest.ENZYME_CLEAVAGE_RULES.keys())
self.enzyme_select.setCurrentText(digest.ENZYME_DEFAULT)
self.digestion_label = QtWidgets.QLabel("Digestion")
self.digestion_select = QtWidgets.QComboBox()
self.digestion_select.addItems(["full", "semi", "none"])
self.digestion_select.setCurrentText(digest.DIGESTION_DEFAULT)
self.special_aas_label = QtWidgets.QLabel("Special AAs")
self.special_aas_line_edit = QtWidgets.QLineEdit()
self.special_aas_line_edit.setText(digest.SPECIAL_AAS_DEFAULT)
self.digestion_group_layout.addWidget(self.enzyme_label, 0, 0)
self.digestion_group_layout.addWidget(self.enzyme_select, 0, 1)
self.digestion_group_layout.addWidget(self.min_length_label, 0, 2)
self.digestion_group_layout.addWidget(self.min_length_spinbox, 0, 3)
self.digestion_group_layout.addWidget(self.digestion_label, 0, 4)
self.digestion_group_layout.addWidget(self.digestion_select, 0, 5)
self.digestion_group_layout.addWidget(self.max_cleavages_label, 1, 0)
self.digestion_group_layout.addWidget(self.max_cleavages_spinbox, 1, 1)
self.digestion_group_layout.addWidget(self.max_length_label, 1, 2)
self.digestion_group_layout.addWidget(self.max_length_spinbox, 1, 3)
self.digestion_group_layout.addWidget(self.special_aas_label, 1, 4)
self.digestion_group_layout.addWidget(self.special_aas_line_edit, 1, 5)
for col in range(6):
self.digestion_group_layout.setColumnStretch(col, 1)
def get_params(self):
return ["--min-length", str(self.min_length_spinbox.value()),
"--max-length", str(self.max_length_spinbox.value()),
"--cleavages", str(self.max_cleavages_spinbox.value()),
"--enzyme", self.enzyme_select.currentText(),
"--digestion", self.digestion_select.currentText(),
"--special-aas", self.special_aas_line_edit.text()]
class MainWindow(QtWidgets.QWidget):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.setWindowTitle("Picked group FDR")
self.tabs = QtWidgets.QTabWidget()
self._add_mq_input_tab()
self._add_percolator_input_tab()
self._add_rescoring_input_tab()
self.fasta_widget = FileSelect('fasta', 'Fasta file (*.fasta *.fa)')
self.output_dir_widget = FileSelect('output', '', folder_select=True)
self.digestion_group = DigestionParametersGroup("Digestion parameters")
layout = QtWidgets.QFormLayout()
self.setLayout(layout)
layout.addRow(self.tabs)
layout.addRow(self.fasta_widget.label, self.fasta_widget)
layout.addRow(self.output_dir_widget.label, self.output_dir_widget)
layout.addRow(self.digestion_group)
self._add_run_button(layout)
self._add_log_textarea(layout)
# sets up handler that will be used by QueueListener
# which will update the LogDialog
handler = LogHandler()
handler.setLevel(logging.INFO) # TODO: this doesn't work, debug messages still make it through
handler.emitter.sigLog.connect(self.log_text_area.widget.appendPlainText)
self.q = multiprocessing.Queue()
self.ql = QueueListener(self.q, handler)
self.ql.start()
self.pool = pool.JobPool(processes=1, warningFilter="default", queue=self.q)
self.resize(800, self.height())
def _add_mq_input_tab(self):
self.mq_tab = QtWidgets.QWidget()
self.mq_layout = QtWidgets.QFormLayout()
self.evidence_widget = MultiFileSelect('evidence.txt', 'Tab separated file (*.txt)')
self.mq_layout.addRow(self.evidence_widget.label, self.evidence_widget)
self.mq_tab.setLayout(self.mq_layout)
self.tabs.addTab(self.mq_tab, "MaxQuant input")
def _add_percolator_input_tab(self):
self.percolator_tab = QtWidgets.QWidget()
self.percolator_layout = QtWidgets.QFormLayout()
self.pout_widget = MultiFileSelect('percolator output', '', 'Add both target and decoy results!')
self.percolator_layout.addRow(self.pout_widget.label, self.pout_widget)
self.percolator_tab.setLayout(self.percolator_layout)
self.tabs.addTab(self.percolator_tab, "Percolator input")
def _add_rescoring_input_tab(self):
self.rescoring_tab = QtWidgets.QWidget()
self.rescoring_layout = QtWidgets.QFormLayout()
self.evidence_widget_rescoring = MultiFileSelect('evidence.txt', 'Tab separated file (*.txt)')
self.pout_widget_rescoring = MultiFileSelect('percolator output', '', 'Add both target and decoy results!')
self.rescoring_layout.addRow(self.evidence_widget_rescoring.label, self.evidence_widget_rescoring)
self.rescoring_layout.addRow(self.pout_widget_rescoring.label, self.pout_widget_rescoring)
self.rescoring_tab.setLayout(self.rescoring_layout)
self.tabs.addTab(self.rescoring_tab, "Rescoring input (e.g. Prosit)")
def _add_run_button(self, layout):
self.run_button = QtWidgets.QPushButton("Run")
self.run_button.clicked.connect(self.run_picked)
self.run_button.setContentsMargins(20,100,20,100)
layout.addRow(self.run_button)
def _add_log_textarea(self, layout):
self.log_text_area = QTextEditLogger(self)
self.log_text_area.setLevel(logging.INFO)
self.log_text_area.widget.setMinimumHeight(self.log_text_area.widget.sizeHint().height())
logger.addHandler(self.log_text_area)
self.log_text_widget = QtWidgets.QWidget()
self.log_text_hbox_layout = QtWidgets.QHBoxLayout()
self.log_text_hbox_layout.setContentsMargins(0, 0, 0, 0)
self.log_text_button_vbox_layout = QtWidgets.QVBoxLayout()
self.log_text_button_vbox_layout.setContentsMargins(0, 0, 0, 0)
self.log_text_button_vbox_layout.setAlignment(Qt.AlignTop)
self.log_text_clear_button = QtWidgets.QPushButton("Clear")
self.log_text_clear_button.clicked.connect(lambda: self.log_text_area.widget.clear())
self.log_text_save_button = QtWidgets.QPushButton("Save")
self.log_text_save_button.clicked.connect(self.save_log_file)
self.log_text_button_vbox_layout.addWidget(self.log_text_clear_button)
self.log_text_button_vbox_layout.addWidget(self.log_text_save_button)
self.log_text_hbox_layout.addWidget(self.log_text_area.widget, stretch = 1)
self.log_text_hbox_layout.addLayout(self.log_text_button_vbox_layout)
self.log_text_widget.setLayout(self.log_text_hbox_layout)
layout.addRow(self.log_text_widget)
def get_output_dir(self):
output_dir = QtWidgets.QFileDialog.getExistingDirectory(self, 'Select output folder' , '', QtWidgets.QFileDialog.ShowDirsOnly)
self.output_dir_line_edit.setText(output_dir)
def save_log_file(self):
filename, _ = QtWidgets.QFileDialog.getSaveFileName(self, 'Save log to file', 'picked_protein_group_fdr.log', 'Log file (*.txt *.log)' )
if not filename:
return
logger.info(f"Saved log messages to {filename}")
with open(filename, 'w') as f:
f.write(self.log_text_area.widget.toPlainText())
def set_buttons_enabled_state(self, enable):
self.evidence_widget.setButtonsEnabled(enable)
self.pout_widget.setButtonsEnabled(enable)
self.evidence_widget_rescoring.setButtonsEnabled(enable)
self.pout_widget_rescoring.setButtonsEnabled(enable)
self.fasta_widget.setButtonsEnabled(enable)
self.output_dir_widget.setButtonsEnabled(enable)
# Cannot stop a QThread if it doesn't have an own event loop
self.run_button.clicked.disconnect()
if enable:
self.run_button.setText("Run")
self.run_button.clicked.connect(self.run_picked)
else:
self.run_button.setText("Stop")
self.run_button.clicked.connect(self.stop_picked)
def run_picked(self):
fasta_file = self.fasta_widget.get_file()
output_dir = self.output_dir_widget.get_file()
digest_params = self.digestion_group.get_params()
evidence_files, pout_files = list(), list()
if self.tabs.currentIndex() == 2:
input_type = "rescoring"
evidence_files = self.evidence_widget_rescoring.get_files()
pout_files = self.pout_widget_rescoring.get_files()
elif self.tabs.currentIndex() == 1:
input_type = "percolator"
pout_files = self.pout_widget.get_files()
else:
input_type = "mq"
evidence_files = self.evidence_widget.get_files()
self.set_buttons_enabled_state(False)
self.pool.applyAsync(run_picked_group_fdr_all, (evidence_files, pout_files, fasta_file, output_dir, digest_params, input_type), callback=self.on_picked_finished)
def on_picked_finished(self, return_code):
self.set_buttons_enabled_state(True)
def stop_picked(self):
self.pool.stopPool()
self.on_picked_finished(-2)
logger.info("Picked Group FDR stopped by user")
self.pool = pool.JobPool(processes=1, warningFilter="default", queue=self.q)
def closeEvent(self, _):
self.stop_picked()
if __name__ == '__main__':
if sys.platform.startswith('win'):
# On Windows calling this function is necessary when combined with pyinstaller:
# https://stackoverflow.com/questions/24944558/pyinstaller-built-windows-exe-fails-with-multiprocessing
multiprocessing.freeze_support()
else:
# On Linux calling this function is necessary when combined with pyqt:
# https://stackoverflow.com/questions/29556291/multiprocessing-with-qt-works-in-windows-but-not-linux
multiprocessing.set_start_method('spawn', force=True)
app = QtWidgets.QApplication(sys.argv)
w = MainWindow()
w.show()
app.exec()