generateLib.py

import GlobalSettings
import os
from PyQt5 import QtWidgets, Qt, uic, QtCore
from functools import partial
from CSPRparser import CSPRparser
import re
import platform
import traceback
import math
from annotation_functions import *

#global logger
logger = GlobalSettings.logger

# Class Name: genLibrary
# this class is a window that allows the user to select the settings for Generate Library
# When the user clicks Generate Library, it goes ahead and gets the Annotation Data needed
#   Then the user can select the settings they want, and then hit submit.
#   It creates a txt file with the data
class genLibrary(QtWidgets.QMainWindow):

    def __init__(self):
        try:
            # qt stuff
            super(genLibrary, self).__init__()
            uic.loadUi(GlobalSettings.appdir + 'generate_library.ui', self)
            self.setWindowTitle('Generate Library')
            self.setWindowIcon(Qt.QIcon(GlobalSettings.appdir + 'cas9image.ico'))

            groupbox_style = """
            QGroupBox:title{subcontrol-origin: margin;
                            left: 10px;
                            padding: 0 5px 0 5px;}
            QGroupBox#Step1{border: 2px solid rgb(111,181,110);
                            border-radius: 9px;
                            font: bold 14pt 'Arial';
                            margin-top: 10px;}"""
            self.Step1.setStyleSheet(groupbox_style)
            self.Step2.setStyleSheet(groupbox_style.replace("Step1", "Step2"))
            self.Step3.setStyleSheet(groupbox_style.replace("Step1", "Step3"))
            self.Step4.setStyleSheet(groupbox_style.replace("Step1", "Step4"))


            # button connections
            self.cancel_button.clicked.connect(self.cancel_function)
            self.BrowseButton.clicked.connect(self.browse_function)
            self.submit_button.clicked.connect(self.submit_data)
            self.progressBar.setValue(0)

            # variables
            self.anno_data = dict()
            self.kegg_nonKegg = ''
            self.gen_lib_dict = dict()
            self.cspr_data = dict()
            self.Output = dict()
            self.off_tol = .05
            self.off_max_misMatch = 4
            self.off_target_running = False
            self.parser = CSPRparser("")

            # set the numbers for the num genes combo box item
            for i in range(10):
                self.numGenescomboBox.addItem(str(i + 1))

            # set the numbers for the minOn combo box
            for i in range(19, 70):
                self.minON_comboBox.addItem(str(i + 1))

            #scale UI
            self.scaleUI()

        except Exception as e:
            logger.critical("Error initializing generate library class.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    #scale UI based on current screen
    def scaleUI(self):
        try:
            self.repaint()
            QtWidgets.QApplication.processEvents()

            screen = QtWidgets.QApplication.desktop().screenNumber(QtWidgets.QApplication.desktop().cursor().pos())
            screen = QtWidgets.QApplication.screens()[screen]
            dpi = screen.physicalDotsPerInch()
            width = screen.geometry().width()
            height = screen.geometry().height()

            # font scaling
            fontSize = 12
            self.fontSize = fontSize
            self.centralWidget().setStyleSheet("font: " + str(fontSize) + "pt 'Arial';")

            #scale title
            fontSize = 30
            self.label.setStyleSheet("font: bold " + str(fontSize) + "pt 'Arial';")

            self.adjustSize()

            currentWidth = self.size().width()
            currentHeight = self.size().height()

            # window scaling
            # 1920x1080 => 800x650
            scaledWidth = int((width * 950) / 1920)
            scaledHeight = int((height * 500) / 1080)

            if scaledHeight < currentHeight:
                scaledHeight = currentHeight
            if scaledWidth < currentWidth:
                scaledWidth = currentWidth

            screen = QtWidgets.QApplication.desktop().screenNumber(QtWidgets.QApplication.desktop().cursor().pos())
            centerPoint = QtWidgets.QApplication.desktop().screenGeometry(screen).center()
            x = centerPoint.x()
            y = centerPoint.y()
            x = x - (math.ceil(scaledWidth / 2))
            y = y - (math.ceil(scaledHeight / 2))
            self.setGeometry(x, y, scaledWidth, scaledHeight)

            self.repaint()
            QtWidgets.QApplication.processEvents()

        except Exception as e:
            logger.critical("Error in scaleUI() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    #center UI on current screen
    def centerUI(self):
        try:
            self.repaint()
            QtWidgets.QApplication.processEvents()

            #center window on current screen
            width = self.width()
            height = self.height()
            screen = QtWidgets.QApplication.desktop().screenNumber(QtWidgets.QApplication.desktop().cursor().pos())
            centerPoint = QtWidgets.QApplication.desktop().screenGeometry(screen).center()
            x = centerPoint.x()
            y = centerPoint.y()
            x = x - (math.ceil(width / 2))
            y = y - (math.ceil(height / 2))
            self.setGeometry(x, y, width, height)

            self.repaint()
            QtWidgets.QApplication.processEvents()
        except Exception as e:
            logger.critical("Error in centerUI() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this function launches the window
    # Parameters:
    #       annotation_data: a dictionary that has the data for the annotations searched for
    #           currently MainWindow's searches dict is passed into this
    #       org_file: the cspr_file that pertains to the organism that user is using at the time
    #       anno_type: whether the user is using KEGG or another type of annotation file
    def launch(self, annotation_data, org_file, anno_type):
        try:
            self.cspr_file = org_file
            self.db_file = org_file[:org_file.find('.')] + '_repeats.db'
            self.anno_data = annotation_data
            self.kegg_nonKegg = anno_type
            self.process = QtCore.QProcess()
            self.parser.fileName = org_file


            # setting the path and file name fields
            index1 = self.cspr_file.find('.')
            if platform.system() == "Windows":
                index2 = self.cspr_file.rfind('\\')
            else:
                index2 = self.cspr_file.rfind('/')

            self.filename_input.setText(self.cspr_file[index2 + 1:index1] + '_lib')


            if platform.system() == "Windows":
                self.output_path.setText(GlobalSettings.CSPR_DB + "\\")
            else:
                self.output_path.setText(GlobalSettings.CSPR_DB + "/")

            # depending on the type of file, build the dictionary accordingly
            self.build_dict_non_kegg()

            # get the gRNA data from the cspr file
            self.cspr_data = self.parser.gen_lib_parser(self.gen_lib_dict, GlobalSettings.mainWindow.endoChoice.currentText())
            self.get_endo_data()

            #center UI
            self.centerUI()
            self.show()
            self.activateWindow()
        except Exception as e:
            logger.critical("Error in launch() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    def get_endo_data(self):
        try:
            f = open(GlobalSettings.appdir + "CASPERinfo")
            self.endo_data = {}
            while True:
                line = f.readline()
                if line.startswith('ENDONUCLEASES'):
                    while True:
                        line = f.readline()
                        line = line.replace("\n","")
                        if (line[0] == "-"):
                            break
                        line_tokened = line.split(";")
                        if len(line_tokened) == 10:
                            endo = line_tokened[0]
                            five_length = line_tokened[2]
                            seed_length = line_tokened[3]
                            three_length = line_tokened[4]
                            prime = line_tokened[5]
                            hsu = line_tokened[9]
                            self.endo_data[endo] = [int(five_length) + int(three_length) + int(seed_length), prime, "MATRIX:" + hsu]

                    break
            f.close()
        except Exception as e:
            logger.critical("Error in get_endo_data() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this is here in case the user clicks 'x' instead of cancel. Just calls the cancel function
    def closeEvent(self, event):
        try:
            closeWindow = self.cancel_function()

            # if the user is doing OT and does not decide to cancel it ignore the event
            if closeWindow == -2:
                event.ignore()
            else:
                event.accept()
        except Exception as e:
            logger.critical("Error in closeEvent() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this function takes all of the cspr data and compresses it again for off-target usage
    def compress_file_off(self):
        try:
            if platform.system() == "Windows":
                file = GlobalSettings.CSPR_DB + "\\off_input.txt"
            else:
                file = GlobalSettings.CSPR_DB + "/off_input.txt"
            f = open(file, 'w')
            for gene in self.cspr_data:
                for j in range(len(self.cspr_data[gene])):
                    loc = self.cspr_data[gene][j][0]
                    seq = self.cspr_data[gene][j][1]
                    pam = self.cspr_data[gene][j][2]
                    score = self.cspr_data[gene][j][3]
                    strand = self.cspr_data[gene][j][4]
                    output = str(loc) + ';' + str(seq) + ';' + str(pam) + ';' + str(score) + ';' + str(strand)
                    f.write(output + '\n')
            f.close()
        except Exception as e:
            logger.critical("Error in compress_file_off() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this function parses the temp_off file, which holds the off-target analysis results
    # it also updates each target in the cspr_data dictionary to replace the endo with the target's results in off-target
    def parse_off_file(self):
        try:
            if platform.system() == "Windows":
                file = GlobalSettings.CSPR_DB + "\\temp_off.txt"
            else:
                file = GlobalSettings.CSPR_DB + "/temp_off.txt"
            f = open(file, "r")
            file_data = f.read().split('\n')
            f.close()
            scoreDict = dict()

            # get the data from the file
            for i in range(len(file_data)):
                if file_data[i] == 'AVG OUTPUT':
                    continue
                elif file_data[i] != '':
                    buffer = file_data[i].split(':')
                    scoreDict[buffer[0]] = buffer[1]

            # update cspr_Data
            for gene in self.cspr_data:
                for i in range(len(self.cspr_data[gene])):
                    tempTuple = (self.cspr_data[gene][i][0], self.cspr_data[gene][i][1], self.cspr_data[gene][i][2], self.cspr_data[gene][i][3], self.cspr_data[gene][i][4], scoreDict[self.cspr_data[gene][i][1]])
                    self.cspr_data[gene][i] = tempTuple
        except Exception as e:
            logger.critical("Error in parse_off_file() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this function runs the off_target command
    # NOTE: some changes may be needed to get it to work with other OS besides windows
    def get_offTarget_data(self, num_targets, minScore, spaceValue, output_file, fiveseq):
        try:
            self.perc = False
            self.bool_temp = False
            self.running = False

            # when finished, parse the off file, and then generate the lib
            def finished():
                if self.off_target_running:
                    self.progressBar.setValue(100)
                    self.parse_off_file()
                    did_work = self.generate(num_targets, minScore, spaceValue, output_file, fiveseq)
                    self.off_target_running = False
                    #self.process.kill()
                    if did_work != -1:
                        self.cancel_function()
                        msgBox = QtWidgets.QMessageBox()
                        msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                        msgBox.setIcon(QtWidgets.QMessageBox.Icon.Information)
                        msgBox.setWindowTitle("Library Generated!")
                        msgBox.setText(
                            "CASPER has finished generating your library!")
                        msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                        msgBox.exec()

                        os.remove(GlobalSettings.CSPR_DB + '/off_input.txt')
                        os.remove(GlobalSettings.CSPR_DB + '/temp_off.txt')

            # as off-targeting outputs things, update the off-target progress bar
            def progUpdate(p):
                line = str(self.process.readAllStandardOutput())
                line = line[2:]
                line = line[:len(line) - 1]
                if platform.system() == 'Windows':
                    for lines in filter(None, line.split(r'\r\n')):
                        if (lines.find("Running Off Target Algorithm for") != -1 and self.perc == False):
                            self.perc = True
                        if (self.perc == True and self.bool_temp == False and lines.find(
                                "Running Off Target Algorithm for") == -1):
                            lines = lines[32:]
                            lines = lines.replace("%", "")
                            if (float(lines) <= 99.5):
                                num = float(lines)
                                self.progressBar.setValue(num)
                            else:
                                self.bool_temp = True
                else:
                    for lines in filter(None, line.split(r'\n')):
                        if (lines.find("Running Off Target Algorithm for") != -1 and self.perc == False):
                            self.perc = True
                        if (self.perc == True and self.bool_temp == False and lines.find(
                                "Running Off Target Algorithm for") == -1):
                            lines = lines[32:]
                            lines = lines.replace("%", "")
                            if (float(lines) <= 99.5):
                                num = float(lines)
                                self.progressBar.setValue(num)
                            else:
                                self.bool_temp = True

            if platform.system() == 'Windows':
                app_path = GlobalSettings.appdir
                exe_path = app_path + 'OffTargetFolder\\OT_Win.exe'
                output_path = '"' + GlobalSettings.CSPR_DB + '\\temp_off.txt" '
                data_path = '"' + GlobalSettings.CSPR_DB + "\\off_input.txt" + '" '
            elif platform.system() == 'Linux':
                app_path = GlobalSettings.appdir.replace('\\', '/')
                exe_path = app_path + r'OffTargetFolder/OT_Lin'
                output_path = '"' + GlobalSettings.CSPR_DB + '/temp_off.txt" '
                data_path = '"' + GlobalSettings.CSPR_DB + "/off_input.txt" + '" '
            else:
                app_path = GlobalSettings.appdir.replace('\\', '/')
                exe_path = app_path + r'OffTargetFolder/OT_Mac'
                output_path = '"' + GlobalSettings.CSPR_DB + '/temp_off.txt" '
                data_path = '"' + GlobalSettings.CSPR_DB + "/off_input.txt" + '" '
            exe_path = '"' + exe_path + '" '
            cspr_path = '"' + self.cspr_file + '" '
            db_path = '"' + self.db_file + '" '
            filename = output_path
            filename = filename[:len(filename) - 1]
            filename = filename[1:]
            filename = filename.replace('"', '')
            CASPER_info_path = '"' + app_path + 'CASPERinfo' +'" '
            num_of_mismathes = self.off_max_misMatch
            tolerance = self.off_tol  # create command string
            endo = '"' + GlobalSettings.mainWindow.endoChoice.currentText() + '" '
            detailed_output = " False "
            avg_output = "True"
            hsu = ' "' + self.endo_data[GlobalSettings.mainWindow.endoChoice.currentText()][2] + '"'

            # set the off_target_running to true, to keep the user from closing the window while it is running
            self.off_target_running = True

            cmd = exe_path + data_path + endo + cspr_path + db_path + output_path + CASPER_info_path + str(
                num_of_mismathes) + ' ' + str(tolerance) + detailed_output + avg_output + hsu

            if platform.system() == 'Windows':
                cmd = cmd.replace('/', '\\')
            self.process.readyReadStandardOutput.connect(partial(progUpdate, self.process))
            self.process.readyReadStandardError.connect(partial(progUpdate, self.process))
            self.progressBar.setValue(0)
            QtCore.QTimer.singleShot(100, partial(self.process.start, cmd))
            self.process.finished.connect(finished)
        except Exception as e:
            logger.critical("Error in get_offTarget_data() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # submit function
    # this function takes all of the input from the window, and calls the generate function
    # Still need to add the checks for 5' seq, and the percentage thing
    def submit_data(self):
        try:
            if self.off_target_running:
                return
            output_file = self.output_path.text() + self.filename_input.text()

            minScore = int(self.minON_comboBox.currentText())
            num_targets = int(self.numGenescomboBox.currentText())
            fiveseq = ''

            # error check for csv files
            if output_file.endswith('.txt'):
                output_file = output_file.replace('.txt', '.csv')
            elif not output_file.endswith('.txt') and not output_file.endswith('.csv'):
                output_file = output_file + '.csv'

            # error checking for the space value
            # if they enter nothing, default to 15 and also make sure it's actually a digit
            if self.space_line_edit.text() == '':
                spaceValue = 15
            elif self.space_line_edit.text().isdigit():
                spaceValue = int(self.space_line_edit.text())
            elif not self.space_line_edit.text().isdigit():
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Error")
                msgBox.setText(
                    "Please enter integers only for space between guides.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return
            # if space value is more than 200, default to 200
            if spaceValue > 200:
                spaceValue = 200
            elif spaceValue < 0:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Error")
                msgBox.setText(
                    "Please enter a space-value that is 0 or greater.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return

            if self.find_off_Checkbox.isChecked():
                self.compress_file_off()



            # get the fiveprimseq data and error check it
            if self.fiveprimeseq.text() != '' and self.fiveprimeseq.text().isalpha():
                fiveseq = self.fiveprimeseq.text()
            elif self.fiveprimeseq.text() != '' and not self.fiveprimeseq.text().isalpha():
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Error")
                msgBox.setText(
                    "Please make sure only the letters A, T, G, or C are added into 5' End specificity box.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return


            # get the targeting range data, and error check it here
            if not self.start_target_range.text().isdigit() or not self.end_target_range.text().isdigit():
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Error")
                msgBox.setText(
                    "Error: Please make sure that the start and end target ranges are numbers only. Please make sure that start is 0 or greater, and end is 100 or less. ")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return
            elif int(self.start_target_range.text()) >= int(self.end_target_range.text()):
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Error")
                msgBox.setText(
                    "Please make sure that the start number is always less than the end number")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return


            # if they check Off-Targeting
            if self.find_off_Checkbox.isChecked():
                # make sure its a digit
                if self.maxOFF_comboBox.text() == '' or not self.maxOFF_comboBox.text().isdigit() and '.' not in self.maxOFF_comboBox.text():
                    msgBox = QtWidgets.QMessageBox()
                    msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                    msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                    msgBox.setWindowTitle("Error")
                    msgBox.setText(
                        "Please enter only numbers for Maximum Off-Target Score. It cannot be left blank")
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                    msgBox.exec()

                    return
                else:
                    # make sure it between 0 and .5
                    if not 0.0 < float(self.maxOFF_comboBox.text()) <= .5:
                        msgBox = QtWidgets.QMessageBox()
                        msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                        msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                        msgBox.setWindowTitle("Error")
                        msgBox.setText(
                            "Please enter a max off-target score between 0 and 0.5!")
                        msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                        msgBox.exec()

                        return
                    # compress the data, and then run off-targeting
                    self.compress_file_off()
                    self.get_offTarget_data(num_targets, minScore, spaceValue, output_file, fiveseq)
            else:
            # actually call the generate function
                did_work = self.generate(num_targets, minScore, spaceValue, output_file, fiveseq)

                if did_work != -1:
                    self.cancel_function()
                    msgBox = QtWidgets.QMessageBox()
                    msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                    msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                    msgBox.setWindowTitle("Library Generated!")
                    msgBox.setText(
                        "CASPER has finished generating your library!")
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                    msgBox.exec()

        except Exception as e:
            logger.critical("Error in submit_data() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # cancel function
    # clears everything and hides the window
    def cancel_function(self):
        try:
            if self.off_target_running:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("Off-Targeting is running")
                msgBox.setText(
                    "Off-Targetting is running. Closing this window will cancel that process, and return to the main window. .\n Do you wish to continue?")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                msgBox.exec()

                if (msgBox.result() == QtWidgets.QMessageBox.No):
                        return -2
                else:
                    self.off_target_running = False
                    self.process.kill()

            self.cspr_file = ''
            self.anno_data = list()

            self.filename_input.setText('')
            self.output_path.setText('')

            self.gen_lib_dict.clear()
            self.cspr_data.clear()
            self.Output.clear()

            self.start_target_range.setText('0')
            self.end_target_range.setText('100')
            self.space_line_edit.setText('15')
            self.find_off_Checkbox.setChecked(False)
            self.modifyParamscheckBox.setChecked(False)
            self.maxOFF_comboBox.setText('')
            self.fiveprimeseq.setText('')
            self.off_target_running = False
            self.progressBar.setValue(0)

            self.hide()
        except Exception as e:
            logger.critical("Error in cancel_function() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # browse function
    # allows the user to browse for a folder
    # stores their selection in the output_path line edit
    def browse_function(self):
        try:
            if self.off_target_running:
                return
            # get the folder
            filed = QtWidgets.QFileDialog()
            mydir = QtWidgets.QFileDialog.getExistingDirectory(filed, "Open a Folder",
                                                           GlobalSettings.CSPR_DB, QtWidgets.QFileDialog.ShowDirsOnly)
            if(os.path.isdir(mydir) == False):
                return

            # make sure to append the '/' to the folder path
            if platform.system() == "Windwos":
                self.output_path.setText(mydir + "\\")
            else:
                self.output_path.setText(mydir + "/")
        except Exception as e:
            logger.critical("Error in browse_function() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # this function builds the dictionary that is used in the generate function
    # this is the version that builds it from data from feature_table, gbff, or gff
    # builds it exactly as Brian built it in the files given
    def build_dict_non_kegg(self):
        try:
            for tuple in self.anno_data:
                chrom = tuple[0]
                feature = tuple[1]
                feature_id = get_id(feature)
                feature_name = get_name(feature)
                feature_desc = get_description(feature)
                ### Order: chromosome number, gene start, gene end, dir of gene, gene description, gene name/locus tag
                self.gen_lib_dict[feature_name] = [chrom,int(feature.location.start),int(feature.location.end),get_strand(feature),get_description(feature),get_name(feature)]
        except Exception as e:
            logger.critical("Error in build_dict_non_kegg() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)

    # generate function taken from Brian's code
    def generate(self,num_targets_per_gene, score_limit, space, output_file, fiveseq):
        try:
            deletedDict = dict()

            # check and see if we need to search based on target_range
            startNum = float(self.start_target_range.text())
            endNum = float(self.end_target_range.text())
            checkStartandEndBool = False
            if startNum != 0.0 or endNum != 100.0:
                if startNum >= 0.0 and endNum <= 100.0:
                    startNum = startNum / 100
                    endNum = endNum / 100
                    checkStartandEndBool = True
                else:
                    msgBox = QtWidgets.QMessageBox()
                    msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                    msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                    msgBox.setWindowTitle("Invalid Targeting Range:")
                    msgBox.setText(
                        "Please select a targeting range between 0 and 100.")
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                    msgBox.exec()

                    return -1

            for gene in self.gen_lib_dict:
                target_list = self.cspr_data[gene]  # Gets the gRNAs for given gene

                #target_list = chrom_list[k:l+1]
                # Reverse the target list if the gene is on negative strand:
                if self.gen_lib_dict[gene][3] == "-":
                    target_list.reverse()

                # Filter out the guides with low scores and long strings of T's
                # also store the ones deleted if the user selects 'modify search parameters'
                if self.modifyParamscheckBox.isChecked():
                    deletedDict[gene] = list()
                for i in range(len(target_list) - 1, -1, -1): ### Start at end and move backwards through list
                    # check the target_range here
                    if int(target_list[i][3]) < int(score_limit):
                        if self.modifyParamscheckBox.isChecked():
                            deletedDict[gene].append(target_list[i])
                        target_list.pop(i)
                    # check for gRNAs with poly T regions here
                    elif re.search("T{5,10}", target_list[i][1]) is not None:
                        if self.modifyParamscheckBox.isChecked():
                            deletedDict[gene].append(target_list[i])
                        target_list.pop(i)

                # check for the fiveseq
                if fiveseq != '':
                    for i in range(len(target_list) - 1, -1, -1): ### Start at end and move backwards through list
                        if not target_list[i][1].startswith(fiveseq.upper()):
                            if self.modifyParamscheckBox.isChecked():
                                deletedDict[gene].append(target_list[i])
                            target_list.pop(i)
                # check the target range here
                if checkStartandEndBool:
                    for i in range(len(target_list) - 1, -1, -1):
                        totalDistance = self.gen_lib_dict[gene][2] - self.gen_lib_dict[gene][1]
                        target_loc = abs(int(target_list[i][0])) - int(self.gen_lib_dict[gene][1])
                        myRatio = target_loc / totalDistance

                        if not (startNum <= myRatio <= endNum):
                            if self.modifyParamscheckBox.isChecked():
                                deletedDict[gene].append(target_list[i])
                            target_list.pop(i)
                # if the user selected off-targeting, check to see that the targets do not exceed the selected max score
                if self.find_off_Checkbox.isChecked():
                    maxScore = float(self.maxOFF_comboBox.text())
                    for i in range(len(target_list) - 1, -1, -1):
                        if maxScore < float(target_list[i][5]):
                            if self.modifyParamscheckBox.isChecked():
                                deletedDict[gene].append(target_list[i])
                            target_list.pop(i)
                # Now generating the targets
                self.Output[gene] = list()
                i = 0
                vec_index = 0
                prev_target = (0, "xyz", 'abc', 1, "-")
                while i < num_targets_per_gene:
                    # select the first five targets with the score and space filter that is set in the beginning
                    if len(target_list) == 0 or vec_index >= len(target_list):
                        break
                    while abs(int(target_list[vec_index][0]) - int(prev_target[0])) < int(space):
                        if target_list[vec_index][3] > prev_target[3] and prev_target != (0,"xyz", "abc", 1, "-"):
                            self.Output[gene].remove(prev_target)
                            self.Output[gene].append(target_list[vec_index])
                            prev_target = target_list[vec_index]
                        vec_index += 1
                        # check and see if there will be a indexing error
                        if vec_index >= len(target_list) - 1:
                            vec_index = vec_index - 1
                            break
                    # Add the new target to the output and add another to i
                    self.Output[gene].append(target_list[vec_index])
                    prev_target = target_list[vec_index]
                    i += 1
                    vec_index += 1

            # if the user selects modify search parameters, go through and check to see if each one has the number of targets that the user wanted
            # if not, append from the deletedDict until they do
            if self.modifyParamscheckBox.isChecked():
                for gene in self.Output:
                    if len(self.Output[gene]) < num_targets_per_gene:
                        for i in range(len(deletedDict[gene])):
                            if len(self.Output[gene]) == num_targets_per_gene:
                                break
                            else:
                                loc = deletedDict[gene][i][0]
                                seq = deletedDict[gene][i][1]
                                pam = deletedDict[gene][i][2]
                                score = deletedDict[gene][i][3]
                                strand = deletedDict[gene][i][4] + '*'
                                endo = deletedDict[gene][i][5]
                                self.Output[gene].append((loc, seq, pam, score, strand, endo))

            # Now output to the file
            try:
                f = open(output_file, 'w')
                # if OT checked
                if self.find_off_Checkbox.isChecked():
                    f.write('Gene Name,Sequence,On-Target Score,Off-Target Score,Location,PAM,Strand\n')
                elif not self.find_off_Checkbox.isChecked():
                    f.write('Gene Name,Sequence,On-Target Score,Location,PAM,Strand\n')

                for gene in self.Output:
                    i = 0
                    gene_name = self.gen_lib_dict[gene][-1]
                    for target in self.Output[gene]:
                        # check to see if the target did not match the user's parameters and they selected 'modify'
                        # if the target has an error, put 2 asterisks in front of the target sequence
                        if '*' in target[4]:
                            tag_id = "**" + gene_name + "-" + str(i + 1)
                        else:
                            tag_id = gene_name + "-" + str(i + 1)
                        i += 1

                        tag_id = tag_id.replace(',', '')

                        # if OT checked
                        if self.find_off_Checkbox.isChecked():
                            f.write(tag_id + ',' + target[1] + ',' + str(target[3]) + ',' + str(target[5]) + ',' + str(abs(int(target[0]))) + ',' + target[2] + ',' + target[4][0] + '\n')
                        # if OT not checked
                        elif not self.find_off_Checkbox.isChecked():
                            f.write(tag_id + ',' + target[1] + ',' + str(target[3]) + ',' + str(abs(int(target[0]))) + ',' + target[2] + ',' + target[4][0] + '\n')

                f.close()
            except PermissionError:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("File Cannot Open")
                msgBox.setText(
                    "This file cannot be opened. Please make sure that the file is not opened elsewhere and try again.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

                return -1
            except Exception as e:
                print(e)
                return
        except Exception as e:
            logger.critical("Error in generate() in generate library.")
            logger.critical(e)
            logger.critical(traceback.format_exc())
            msgBox = QtWidgets.QMessageBox()
            msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
            msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
            msgBox.setWindowTitle("Fatal Error")
            msgBox.setText("Fatal Error:\n"+str(e)+ "\n\nFor more information on this error, look at CASPER.log in the application folder.")
            msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Close)
            msgBox.exec()

            exit(-1)