NewGenome.py

from ast import Global
import os
from PyQt5 import QtWidgets, uic, QtGui, QtCore, Qt
import GlobalSettings
from functools import partial
from Algorithms import SeqTranslate
import webbrowser
import platform
import traceback
import math

#global logger
logger = GlobalSettings.logger

def iter_except(function, exception):
    """Works like builtin 2-argument `iter()`, but stops on `exception`."""
    try:
        while True:
            yield function()
    except exception:
        return


#UI prompt for when the user has finished running jobs in new genome to allow them to choose where the want to proceed
class goToPrompt(QtWidgets.QMainWindow):
    def __init__(self):
        try:
            super(goToPrompt, self).__init__()
            uic.loadUi(GlobalSettings.appdir + 'newgenomenavigationpage.ui', self)

            groupbox_style = """
            QGroupBox:title{subcontrol-origin: margin;
                            left: 10px;
                            padding: 0 5px 0 5px;}
            QGroupBox#groupBox{border: 2px solid rgb(111,181,110);
                            border-radius: 9px;
                            font: bold 14pt 'Arial';
                            margin-top: 10px;}"""
            self.groupBox.setStyleSheet(groupbox_style)
            self.scaleUI()
            self.setWindowTitle("New Genome")
            self.setWindowIcon(Qt.QIcon(GlobalSettings.appdir + "cas9image.ico"))
            self.hide()

        except Exception as e:
            logger.critical("Unable to initialize goToPrompt class in New Genome.")
            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 = self.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';")

            self.adjustSize()

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

            # window scaling
            # 1920x1080 => 550x200
            scaledWidth = int((width * 575) / 1920)
            scaledHeight = int((height * 175) / 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 new genome navigation window.")
            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 new genome navigation window.")
            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)


#New genome class to allow users to generate new CSPR files
class NewGenome(QtWidgets.QMainWindow):

    #init class
    def __init__(self, info_path):
        try:
            super(NewGenome, self).__init__()
            uic.loadUi(GlobalSettings.appdir + 'NewGenome.ui', self)
            self.setWindowTitle('New Genome')
            self.setWindowTitle('New Genome')
            self.info_path = info_path

            #---Style Modifications---#

            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"))

            #---Button Modifications---#

            self.setWindowIcon(Qt.QIcon(GlobalSettings.appdir + "cas9image.ico"))
            self.resetButton.clicked.connect(self.reset)
            self.submitButton.clicked.connect(self.submit)
            self.browseForFile.clicked.connect(self.selectFasta)
            self.remove_job.clicked.connect(self.remove_from_queue)
            self.output_browser.setText("Waiting for program initiation...")
            self.contButton.clicked.connect(self.continue_to_main)

            self.comboBoxEndo.currentIndexChanged.connect(self.endo_settings)

            self.runButton.clicked.connect(self.run_jobs_wrapper)
            self.clearButton.clicked.connect(self.clear_all)

            self.JobsQueue = []  # holds Job classes.
            self.check_strings = []
            self.Endos = dict()
            self.file = ""

            self.process = QtCore.QProcess()
            self.process.setProcessChannelMode(QtCore.QProcess.MergedChannels)
            self.process.finished.connect(self.upon_process_finishing)
            self.seqTrans = SeqTranslate()
            self.exit = False


            self.first = False
            #show functionalities on window
            self.fillEndo()

            self.num_chromo_next = False

            #Jobs Table
            self.job_Table.setShowGrid(False)
            self.job_Table.horizontalHeader().setSectionsClickable(True)
            self.job_Table.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
            self.job_Table.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
            self.job_Table.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
            self.job_Table.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents)
            self.fin_index=0


            self.mwfg = self.frameGeometry()  ##Center window
            self.cp = QtWidgets.QDesktopWidget().availableGeometry().center()  ##Center window
            self.total_chrom_count = 0
            self.perc_increase = 0
            self.progress = 0

            #toolbar button actions
            self.visit_repo.triggered.connect(self.visit_repo_func)
            self.go_ncbi.triggered.connect(self.open_ncbi_web_page)

            self.comboBoxEndo.currentIndexChanged.connect(self.changeEndos)

            ### NCBI tool
            self.NCBI_File_Search.clicked.connect(self.open_ncbi_tool)

            self.seed_length.setEnabled(False)
            self.five_length.setEnabled(False)
            self.three_length.setEnabled(False)
            self.repeats_box.setEnabled(False)

            ### User prompt class
            self.goToPrompt = goToPrompt()
            self.goToPrompt.goToMain.clicked.connect(self.continue_to_main)
            self.goToPrompt.goToMT.clicked.connect(self.continue_to_MT)
            self.goToPrompt.goToPop.clicked.connect(self.continue_to_pop)

            self.orgName.setFocus()

            ### Connect New endonuclease to New Genome
            self.actionUpload_New_Endonuclease.triggered.connect(self.launch_newEndonuclease)

            ### Set up validators for input fields:
            reg_ex1 = QtCore.QRegExp("[^/\\\\_]+") # No slashes or underscores
            reg_ex2 = QtCore.QRegExp("\\S+")
            input_validator1 = QtGui.QRegExpValidator(reg_ex1, self)
            input_validator2 = QtGui.QRegExpValidator(reg_ex2, self)
            self.orgName.setValidator(input_validator1)
            self.strainName.setValidator(input_validator1)
            self.orgCode.setValidator(input_validator2)

            ### Scale UI
            self.scaleUI()
            self.first_show = True

        except Exception as e:
            logger.critical("Unable to initialize New Genome 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)

    def launch_newEndonuclease(self):
        try:
            GlobalSettings.mainWindow.getData()
            GlobalSettings.mainWindow.newEndonuclease.centerUI()
            GlobalSettings.mainWindow.newEndonuclease.show()
            GlobalSettings.mainWindow.newEndonuclease.activateWindow()
        except Exception as e:
            logger.critical("Error in launch_newEndonuclease() in New Genome.")
            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 the UI
    def scaleUI(self):
        try:
            self.repaint()
            QtWidgets.QApplication.processEvents()

            screen = self.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';")
            self.menuBar().setStyleSheet("font: " + str(fontSize) + "pt 'Arial';")

            # CASPER header scaling
            fontSize = 30
            self.label_8.setStyleSheet("font: bold " + str(fontSize) + "pt 'Arial';")

            self.adjustSize()

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

            # window scaling
            # 1920x1080 => 850x750
            scaledWidth = int((width * 850) / 1920)
            scaledHeight = int((height * 750) / 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 new genome.")
            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 the 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 new genome.")
            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)

    #open the ncbi search tool window
    def open_ncbi_tool(self):
        try:
            #center ncbi on current screen
            if GlobalSettings.mainWindow.ncbi.first_show == True:
                GlobalSettings.mainWindow.ncbi.first_show = False
                GlobalSettings.mainWindow.ncbi.centerUI()
            if self.orgName.text() != "":
                GlobalSettings.mainWindow.ncbi.organism_line_edit.setText(self.orgName.text())
            if self.strainName.text() != "":
                GlobalSettings.mainWindow.ncbi.infra_name_line_edit.setText(self.strainName.text())
            GlobalSettings.mainWindow.ncbi.show()
            GlobalSettings.mainWindow.ncbi.activateWindow()
        except Exception as e:
            logger.critical("Error in open_ncbi_tool() in New Genome.")
            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)

    #remove jobs from queue
    def remove_from_queue(self):
        try:
            while(True):
                indexes = self.job_Table.selectionModel().selectedRows()
                if len(indexes) == 0:
                    break
                self.job_Table.removeRow(indexes[0].row())
        except Exception as e:
            logger.critical("Error in remove_from_queue() in New Genome.")
            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)

    #prompt user with file browser to select fasta/fna files
    def selectFasta(self):
        try:
            filed = QtWidgets.QFileDialog()
            myFile = QtWidgets.QFileDialog.getOpenFileName(filed, "Choose a File")
            if (myFile[0] != ""):
                if not myFile[0].endswith(".fa") and not myFile[0].endswith(".fna") and not myFile[0].endswith(".fasta"):
                    msgBox = QtWidgets.QMessageBox()
                    msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                    msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                    msgBox.setWindowTitle("File Selection Error")
                    msgBox.setText("You have selected an incorrect type of file. Please choose a FASTA/FNA file.")
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                    msgBox.exec()

                    return
                else:
                    self.file = myFile[0]
                    self.selectedFile.setText(str(myFile[0]))

        except Exception as e:
            logger.critical("Error in selectFasta() in New Genome.")
            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 jobs to queue
    def submit(self):
        try:
            warning = ""
            if len(self.orgName.text()) == 0:
                warning = warning + "You need to include the organism's name."
            if len(self.file) == 0:
                warning = warning + "You need to select a file."
            if len(warning) != 0:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("Required Information")
                msgBox.setText(warning)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()
                return

            if len(self.strainName.text()) == 0:
                warning = warning + "\nIt is recommended to include the organism's subspecies/strain."
            if len(self.orgCode.text()) == 0:
                warning = warning + "\nYou must include an organism code."
            if len(warning) != 0:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("Missing Information")
                msgBox.setText(warning + "\n\nDo you wish to continue without including this information?")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                msgBox.exec()

                if msgBox.result() == QtWidgets.QMessageBox.No:
                    return



            #endo, pam, repeats, directionality, five length, seed length, three length, orgcode, output path, CASPERinfo path, fna path, orgName, notes, on target matrix
            args = self.Endos[self.comboBoxEndo.currentText()][0]
            args += " " + self.Endos[self.comboBoxEndo.currentText()][1]
            if self.mt.isChecked():
                args += " " + "TRUE"
            else:
                args += " " + "FALSE"

            if self.Endos[self.comboBoxEndo.currentText()][5] == "3":
                args += " " + "FALSE"
            else:
                args += " " + "TRUE"

            if self.repeats_box.isChecked():
                args += " " + "TRUE"
            else:
                args += " " + "FALSE"

            args += " " + self.Endos[self.comboBoxEndo.currentText()][2]
            args += " " + self.Endos[self.comboBoxEndo.currentText()][3]
            args += " " + self.Endos[self.comboBoxEndo.currentText()][4]
            args += " " + self.orgCode.text()
            if platform.system() == 'Windows':
                args += " " + '"' + GlobalSettings.CSPR_DB.replace("/","\\") + '\\"'
                args += " " + '"' + GlobalSettings.appdir.replace("/","\\") + "CASPERinfo" + '"'
                args += " " + '"' + self.file.replace("/","\\") + '"'
            else:
                args += " " + '"' + GlobalSettings.CSPR_DB.replace("\\","/") + '/"'
                args += " " + '"' + GlobalSettings.appdir.replace("\\","/") + "CASPERinfo" + '"'
                args += " " + '"' + self.file.replace("\\","/") + '"'

            args += " " + '"' + self.orgName.text() + " " + self.strainName.text() + '"'
            args += " " + '"' + "notes" + '"'
            args += " " + '"DATA:' + self.Endos[self.comboBoxEndo.currentText()][6] + '"'

            tmp = self.orgName.text()+ " " + self.strainName.text() + " " + self.Endos[self.comboBoxEndo.currentText()][0] + " " + self.orgCode.text()
            if tmp in self.check_strings:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("Duplicate Entry")
                msgBox.setText("You have submitted a duplicate entry. Consider changing the organism code or strain name to differentiate closely related strains.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()
                return
            name = self.orgCode.text() + "_" + str(self.Endos[self.comboBoxEndo.currentText()][0])
            rowPosition = self.job_Table.rowCount()
            self.job_Table.insertRow(rowPosition)
            item = QtWidgets.QTableWidgetItem(name)
            item.setTextAlignment(QtCore.Qt.AlignHCenter)
            self.job_Table.setItem(rowPosition, 0, item)
            self.check_strings.append(tmp)
            self.JobsQueue.append(args)
        except Exception as e:
            logger.critical("Error in submit() in New Genome.")
            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)

    #fill the endo dropdown
    def fillEndo(self):
        try:
            #disconnect signal
            try:
                self.comboBoxEndo.currentIndexChanged.disconnect()
            except:
                pass

            #clear out the endo box
            self.comboBoxEndo.clear()

            f = open(GlobalSettings.appdir + "CASPERinfo")
            while True:
                line = f.readline()
                if line.startswith('ENDONUCLEASES'):
                    while True:
                        line = f.readline()
                        if (line[0] == "-"):
                            break
                        line_tokened = line.split(";")
                        if len(line_tokened) == 10:
                            endo = line_tokened[0]
                            # Checking to see if there is more than one pam sequence in the list
                            if line_tokened[1].find(",") != -1:
                                p_pam = line_tokened[1].split(",")[0]
                            else:
                                p_pam = line_tokened[1]
                            five_length = line_tokened[2]
                            seed_length = line_tokened[3]
                            three_length = line_tokened[4]
                            dir = line_tokened[5]
                            on_target_data = line_tokened[8]
                            self.Endos[endo + " - PAM: " + p_pam] = (endo, p_pam, five_length, seed_length, three_length, dir, on_target_data)
                    break
            f.close()
            self.comboBoxEndo.addItems(self.Endos.keys())
            key = list(self.Endos.keys())[0]
            self.seed_length.setText(self.Endos[key][3])
            self.five_length.setText(self.Endos[key][2])
            self.three_length.setText(self.Endos[key][4])

            #reconnect signal
            self.comboBoxEndo.currentIndexChanged.connect(self.changeEndos)
        except Exception as e:
            logger.critical("Error in fillEndo() in New Genome.")
            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)

    #event handler for endo changing - update endo length data
    def changeEndos(self):
        try:
            key = str(self.comboBoxEndo.currentText())
            self.seed_length.setText(self.Endos[key][3])
            self.five_length.setText(self.Endos[key][2])
            self.three_length.setText(self.Endos[key][4])
        except Exception as e:
            logger.critical("Error in changeEndos() in New Genome.")
            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)

    #check if endo is 3' or 5'
    def endo_settings(self):
        try:
            # check the if it's 3' or 5', and check the box accordingly
            if int(self.seqTrans.endo_info[self.Endos[self.comboBoxEndo.currentText()][0]][3]) == 3:
                self.pamBox.setChecked(0)
            elif int(self.seqTrans.endo_info[self.Endos[self.comboBoxEndo.currentText()][0]][3]) == 5:
                self.pamBox.setChecked(1)
        except Exception as e:
            logger.critical("Error in endo_settings() in New Genome.")
            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)

    #wrapper for running jobs
    def run_jobs_wrapper(self):
        try:
            self.indexes = []
            self.job_Table.selectAll()
            indexes = self.job_Table.selectionModel().selectedRows()
            for index in sorted(indexes):
                if self.job_Table.item(index.row(), 0).text() != "":
                    self.indexes.append(index.row())
            self.run_job()
        except Exception as e:
            logger.critical("Error in run_jobs_wrapper() in New Genome.")
            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)

    #run job in queue
    def run_job(self):
        try:
            if len(self.indexes) > 0:
                self.progressBar.setValue(0)
                self.progress = 0
                row_index = self.indexes[0]
                name = self.job_Table.item(row_index, 0).text()
                item = QtWidgets.QTableWidgetItem(name)
                item.setTextAlignment(QtCore.Qt.AlignHCenter)
                self.job_Table.setItem(row_index, 1, item)
                self.job_Table.setItem(row_index, 0, QtWidgets.QTableWidgetItem(""))

                def output_stdout(p):
                    line = str(p.readAll())
                    line = line[2:]
                    line = line[:len(line) - 1]
                    for lines in line.split(r"\n"):
                        lines = lines.rstrip("\n")
                        lines = lines.rstrip("\r")
                        lines = lines.rstrip(r"\n")
                        lines = lines.rstrip(r"\r")
                        lines = lines.rstrip("\r\n")
                        lines = lines.rstrip(r"\r\n")
                        if lines != "":
                            if lines.find("Number of Chromosomes/Scaffolds") != -1:
                                copy = lines
                                copy = copy.replace(" ","")
                                copy = copy[copy.find(":")+1:]
                                self.total_chrom_count = int(copy)
                                self.perc_increase = ((1 / (2 * self.total_chrom_count)) * 70)
                                self.progressBar.setValue(20)
                                self.progress = 20
                            elif lines.find("complete.") != -1:
                                self.progress += self.perc_increase
                                self.progressBar.setValue(int(self.progress))
                            elif lines.find("Processing Targets.") != -1:
                                self.progress = 70
                                self.progressBar.setValue(int(self.progress))
                            elif lines.find("Writing out uniques.") != -1:
                                self.progress = 90
                                self.progressBar.setValue(int(self.progress))
                            elif lines.find("Writing out repeats.") != -1:
                                self.progress = 95
                                self.progressBar.setValue(int(self.progress))
                            elif lines == "Finished.":
                                self.progress = 100
                                self.progressBar.setValue(int(self.progress))
                            self.output_browser.append(lines)

                job_args = self.JobsQueue[row_index]
                if platform.system() == 'Windows':
                    program = '"' + GlobalSettings.appdir + "SeqFinderFolder/Casper_Seq_Finder_Win.exe" + '" '
                elif platform.system() == 'Linux':
                    program = '"' + GlobalSettings.appdir + "SeqFinderFolder/Casper_Seq_Finder_Lin" + '" '
                else:
                    program = '"' + GlobalSettings.appdir + "SeqFinderFolder/Casper_Seq_Finder_Mac" + '" '
                program += job_args
                self.process.readyReadStandardOutput.connect(partial(output_stdout, self.process))
                self.process.start(program)
            else:
                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
                msgBox.setWindowTitle("No Jobs To Run")
                msgBox.setText("No jobs are in the queue to run. Please add a job before running.")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
                msgBox.exec()

        except Exception as e:
            logger.critical("Error in run_job() in New Genome.")
            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)

    #even handler for when jobs finish execution
    def upon_process_finishing(self):
        try:
            row_index = self.indexes[0]
            name = self.job_Table.item(row_index, 1).text()
            item = QtWidgets.QTableWidgetItem(name)
            item.setTextAlignment(QtCore.Qt.AlignHCenter)
            self.job_Table.setItem(row_index, 2, item)
            self.job_Table.setItem(row_index, 1, QtWidgets.QTableWidgetItem(""))
            self.indexes.pop(0)
            if len(self.indexes) != 0:
                self.run_job()
            else:
                #prompt user if they want to analyze their new files
                self.goToPrompt.centerUI()
                self.goToPrompt.show()
                self.goToPrompt.activateWindow()
        except Exception as e:
            logger.critical("Error in upon_process_finishing() in New Genome.")
            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)

    #clear the job table
    def clear_all(self):
        try:
            self.process.kill()
            self.fin_index = 0
            self.job_Table.clearContents()
            self.job_Table.setRowCount(0)
            self.JobsQueue = []
            self.check_strings = []
            self.output_browser.clear()
            self.output_browser.setText("Waiting for program initiation...")
            self.orgName.clear()
            self.strainName.clear()
            self.orgCode.clear()
            self.selectedFile.clear()
            self.selectedFile.setPlaceholderText("Selected FASTA/FNA File")
            self.progressBar.setValue(0)
            self.first = False
        except Exception as e:
            logger.critical("Error in clear_all() in New Genome.")
            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)

    #reset the whole form
    def reset(self):
        try:
            self.orgName.clear()
            self.strainName.clear()
            self.orgCode.clear()
            self.selectedFile.clear()
            self.selectedFile.setPlaceholderText("Selected FASTA/FNA File")
            self.output_browser.clear()
            self.output_browser.setText("Waiting for program initiation...")
            self.file = ""
        except Exception as e:
            logger.critical("Error in reset() in New Genome.")
            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)

    #menu button for launching NCBI web page
    def open_ncbi_web_page(self):
        try:
            webbrowser.open('https://www.ncbi.nlm.nih.gov/', new=2)
        except Exception as e:
            logger.critical("Error in open_ncbi_web_page() in New Genome.")
            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)

    #menu button for launching github repo
    def visit_repo_func(self):
        try:
            webbrowser.open('https://github.com/TrinhLab/CASPERapp')
        except Exception as e:
            logger.critical("Error in visit_repo_func() in New Genome.")
            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)

    #event handler for user wanting to close the window
    def closeEvent(self, event):
        try:
            # make sure that there are cspr files in the DB
            file_names = os.listdir(GlobalSettings.CSPR_DB)
            noCSPRFiles = True
            for file in file_names:
                if 'cspr' in file:
                    noCSPRFiles = False
                    break
            if noCSPRFiles == True:
                if self.exit == False:
                    msgBox = QtWidgets.QMessageBox()
                    msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                    msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                    msgBox.setWindowTitle("No CSPR file generated")
                    msgBox.setText("No CSPR file has been generated, thus the main program cannot run. Please create a CSPR file."
                                                            "Alternatively, you could quit the program. Would you like to quit?")
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                    msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                    msgBox.exec()

                    if (msgBox.result() == QtWidgets.QMessageBox.No):
                        event.ignore()
                    else:
                        event.accept()
                else:
                    self.exit = False
                    event.accept()

            else:
                self.process.kill()
                self.clear_all()
                self.goToPrompt.hide()
                GlobalSettings.mainWindow.fill_annotation_dropdown()
                if GlobalSettings.mainWindow.orgChoice.currentText() != '':
                    GlobalSettings.mainWindow.orgChoice.currentIndexChanged.disconnect()
                GlobalSettings.mainWindow.orgChoice.clear()
                GlobalSettings.mainWindow.endoChoice.clear()
                GlobalSettings.mainWindow.getData()
                GlobalSettings.MTWin.launch()
                GlobalSettings.pop_Analysis.launch()

                if GlobalSettings.mainWindow.first_show == True:
                    GlobalSettings.mainWindow.first_show = False
                    GlobalSettings.mainWindow.centerUI()
                GlobalSettings.mainWindow.show()
                event.accept()
        except Exception as e:
            logger.critical("Error in closeEvent() in New Genome.")
            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)

    #event handler for user wanting to go to Main once jobs complete
    def continue_to_main(self):
        try:
            # make sure that there are cspr files in the DB
            file_names = os.listdir(GlobalSettings.CSPR_DB)
            noCSPRFiles = True
            for file in file_names:
                if 'cspr' in file:
                    noCSPRFiles = False
                    break
            if noCSPRFiles == True:

                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("No CSPR file generated")
                msgBox.setText(
                    "No CSPR file has been generated, thus the main program cannot run. Please create a CSPR file."
                    "Alternatively, you could quit the program. Would you like to quit?")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                msgBox.exec()


                if (msgBox.result() == QtWidgets.QMessageBox.Yes):
                    self.exit = True
                    self.close()

            else:
                self.process.kill()
                self.clear_all()
                self.goToPrompt.hide()
                GlobalSettings.mainWindow.fill_annotation_dropdown()
                if GlobalSettings.mainWindow.orgChoice.currentText() != '':
                    GlobalSettings.mainWindow.orgChoice.currentIndexChanged.disconnect()
                GlobalSettings.mainWindow.orgChoice.clear()
                GlobalSettings.mainWindow.endoChoice.clear()
                GlobalSettings.mainWindow.getData()
                GlobalSettings.MTWin.launch()
                GlobalSettings.pop_Analysis.launch()

                # center main on current screen
                if GlobalSettings.mainWindow.first_show == True:
                    GlobalSettings.mainWindow.first_show = False
                    GlobalSettings.mainWindow.centerUI()
                GlobalSettings.mainWindow.show()
                self.hide()
        except Exception as e:
            logger.critical("Error in continue_to_main() in New Genome.")
            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)

    #event handler for user wanting to go to multi-targeting once jobs complete
    def continue_to_MT(self):
        try:
            # make sure that there are cspr files in the DB
            file_names = os.listdir(GlobalSettings.CSPR_DB)
            noCSPRFiles = True
            for file in file_names:
                if 'cspr' in file:
                    noCSPRFiles = False
                    break
            if noCSPRFiles == True:

                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("No CSPR file generated")
                msgBox.setText(
                    "No CSPR file has been generated, thus the main program cannot run. Please create a CSPR file."
                    "Alternatively, you could quit the program. Would you like to quit?")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                msgBox.exec()



                if (msgBox.result() == QtWidgets.QMessageBox.Yes):
                    self.exit = True
                    self.close()

            else:
                self.process.kill()
                self.clear_all()
                self.goToPrompt.hide()
                GlobalSettings.mainWindow.fill_annotation_dropdown()
                if GlobalSettings.mainWindow.orgChoice.currentText() != '':
                    GlobalSettings.mainWindow.orgChoice.currentIndexChanged.disconnect()
                GlobalSettings.mainWindow.orgChoice.clear()
                GlobalSettings.mainWindow.endoChoice.clear()
                GlobalSettings.mainWindow.getData()
                GlobalSettings.MTWin.launch()
                GlobalSettings.pop_Analysis.launch()

                # center multi-targeting on current screen
                if GlobalSettings.MTWin.first_show == True:
                    GlobalSettings.MTWin.first_show = False
                    GlobalSettings.MTWin.centerUI()

                GlobalSettings.MTWin.show()
                self.hide()
        except Exception as e:
            logger.critical("Error in continue_to_MT() in New Genome.")
            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)

    #event handler for user wanting to go to population analysis once jobs complete
    def continue_to_pop(self):
        try:
            # make sure that there are cspr files in the DB
            file_names = os.listdir(GlobalSettings.CSPR_DB)
            noCSPRFiles = True
            for file in file_names:
                if 'cspr' in file:
                    noCSPRFiles = False
                    break
            if noCSPRFiles == True:

                msgBox = QtWidgets.QMessageBox()
                msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
                msgBox.setIcon(QtWidgets.QMessageBox.Icon.Question)
                msgBox.setWindowTitle("No CSPR file generated")
                msgBox.setText(
                    "No CSPR file has been generated, thus the main program cannot run. Please create a CSPR file."
                    "Alternatively, you could quit the program. Would you like to quit?")
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Yes)
                msgBox.addButton(QtWidgets.QMessageBox.StandardButton.No)
                msgBox.exec()

                if (msgBox.result() == QtWidgets.QMessageBox.Yes):
                    self.exit = True
                    self.close()

            else:
                self.process.kill()
                self.clear_all()
                self.goToPrompt.hide()
                GlobalSettings.mainWindow.fill_annotation_dropdown()
                if GlobalSettings.mainWindow.orgChoice.currentText() != '':
                    GlobalSettings.mainWindow.orgChoice.currentIndexChanged.disconnect()
                GlobalSettings.mainWindow.orgChoice.clear()
                GlobalSettings.mainWindow.endoChoice.clear()
                GlobalSettings.mainWindow.getData()
                GlobalSettings.MTWin.launch()
                GlobalSettings.pop_Analysis.launch()

                if GlobalSettings.pop_Analysis.first_show == True:
                    GlobalSettings.pop_Analysis.first_show = False
                    GlobalSettings.pop_Analysis.centerUI()

                GlobalSettings.pop_Analysis.show()
                self.hide()
        except Exception as e:
            logger.critical("Error in continue_to_pop() in New Genome.")
            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)