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export_tool.py
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export_tool.py
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import GlobalSettings
from Algorithms import get_table_headers
import os
from PyQt5 import QtWidgets, Qt, uic, QtCore, QtGui
import platform
import traceback
import math
#global logger
logger = GlobalSettings.logger
# Class: export_tool
# This class opens a window for the user to select where they want the CSV file exported to, and the name of the file
# It takes the highlighted data from the Results page, and creates a CSV file from that
class export_tool(QtWidgets.QMainWindow):
# init function. Sets all of the buttons
def __init__(self):
try:
# qt stuff
super(export_tool, self).__init__()
uic.loadUi(GlobalSettings.appdir + 'export_tool.ui', self)
self.setWindowIcon(Qt.QIcon(GlobalSettings.appdir + "cas9image.ico"))
# button connections
self.browse_button.clicked.connect(self.browseForFolder)
self.cancel_button.clicked.connect(self.cancel_function)
self.export_button.clicked.connect(self.export_function)
# Set up validators for input fields:
reg_ex = QtCore.QRegExp("[^,]+") # No commas
input_validator = QtGui.QRegExpValidator(reg_ex, self)
self.leading_seq.setValidator(input_validator)
self.trailing_seq.setValidator(input_validator)
# GroupBox styling
groupbox_style = """
QGroupBox:title{subcontrol-origin: margin;
left: 10px;
padding: 0 5px 0 5px;}
QGroupBox#gRNA_Options{border: 2px solid rgb(111,181,110);
border-radius: 9px;
margin-top: 10px;
font: bold 14pt 'Arial';} """
self.gRNA_Options.setStyleSheet(groupbox_style)
# variables
self.location = self.fileLocation_line_edit.text()
self.selected_table_items = []
self.window = ""
self.num_columns = []
self.locus_tag = False
self.gene_name = False
self.setWindowTitle("Export to CSV")
self.scaleUI()
except Exception as e:
logger.critical("Error initializing export_tool 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';")
self.adjustSize()
currentWidth = self.size().width()
currentHeight = self.size().height()
# window scaling
# 1920x1080 => 1150x650
scaledWidth = int((width * 650) / 1920)
scaledHeight = int((height * 200) / 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 export_tool.")
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 export_tool.")
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)
# launch function. Called in Results.
# parameter expect: a list of the items selected from the window.
def launch(self, select_items, window):
try:
if platform.system() == "Windows":
self.fileLocation_line_edit.setText(GlobalSettings.CSPR_DB + "\\")
else:
self.fileLocation_line_edit.setText(GlobalSettings.CSPR_DB + "/")
self.selected_table_items = select_items
self.window = window
self.centerUI()
self.show()
self.activateWindow()
except Exception as e:
logger.critical("Error in launch() in export_tool.")
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)
# export function
# Takes the path and file name and combines them
# Writes the header line, as well as ever line selected to that file
# calls the cancel function when it's done
def export_function(self):
try:
delim = self.delimBox.currentText()
# get the full path ( path and file name)
file_name = self.filename_line_edit.text()
if file_name == "":
file_name = "exported_gRNAs"
self.location = self.fileLocation_line_edit.text()
full_path = ""
if '.' in file_name: # If user added the file extension...
full_path = self.location + file_name
else:
if delim == ",":
full_path = self.location + file_name + '.csv'
elif delim == r"\t":
delim = "\t"
full_path = self.location + file_name + '.tsv'
else:
full_path = self.location + file_name + '.txt'
try:
output_data = open(full_path, 'w')
""" Write the table headers """
if self.window == "mt": ###Change headers for multitargeting table export
headers = get_table_headers(GlobalSettings.MTWin.table)
num_cols = len(headers) # Calculate the number of columns based on the headers list above
insertion_index = headers.index("% Consensus")
headers.insert(insertion_index, "Full Sequence")
output_data.write(delim.join(headers)+"\n")
elif self.window == "pa":
headers = get_table_headers(GlobalSettings.pop_Analysis.table2)
num_cols = len(headers) # Calculate the number of columns based on the headers list above
insertion_index = headers.index("% Consensus")
headers.insert(insertion_index, "Full Sequence")
output_data.write(delim.join(headers)+"\n")
else: ###Change headers for view results export
headers = get_table_headers(GlobalSettings.mainWindow.Results.targetTable)
headers.remove("Details") # For some reason, the details column doesn't carry any "items"
num_cols = len(headers) # Calculate the number of columns based on the headers list above
insertion_index = headers.index("Strand")
headers.insert(insertion_index, "Full Sequence")
if GlobalSettings.mainWindow.radioButton_Gene.isChecked(): # If the user chose to search via Feature
tmp = GlobalSettings.mainWindow.Results.comboBoxGene.currentText().split(":") # Check to see if the locus tag was found for the current gene
if len(tmp) > 1: # If locus tag exists for gene, include in output
headers.extend(["Locus_Tag","Gene_Name"])
output_data.write(delim.join(headers)+"\n")
self.locus_tag = True
self.gene_name = True
else: # If locus tag does not exist for gene, only include the gene name
headers.append("Gene_Name")
output_data.write(delim.join(headers)+"\n")
self.gene_name = True
self.locus_tag = False
else: # If user searched by sequence or position, don't include locus tag or gene name
output_data.write(delim.join(headers)+"\n")
self.gene_name = False
self.locus_tag = False
""" Write the data out """
tmp_list = []
if self.locus_tag: #If the user is exporting data from VT and locus tag exists for current gene
tmp = GlobalSettings.mainWindow.Results.comboBoxGene.currentText().split(":") # Get the locus tag
locus_tag = str(tmp[0].strip())
gene_name = str(tmp[-1].strip())
seq_index = headers.index("Sequence") # Get the gene name
it = 0
for i, item in enumerate(self.selected_table_items): # Loop through all the items in the View Targets table
if (i+1) % num_cols == 0:
tmp_list.append(item.text())
tmp_list.append(locus_tag)
tmp_list.append(gene_name)
output_data.write(delim.join(tmp_list)+"\n") # Write data out
tmp_list.clear() # Reset list
it = 0 # Reset iterator
elif it == seq_index:
tmp_list.append(item.text())
tmp_list.append(self.leading_seq.text().strip() + item.text() + self.trailing_seq.text().strip()) #5' Leader + gRNA + 3' Trailer
it += 1
else:
tmp_list.append(item.text())
it += 1
elif self.gene_name: #If the user is exporting data from VT and locus tag doesn't exist for current gene
gene_name = str(GlobalSettings.mainWindow.Results.comboBoxGene.currentText().strip()) # Get the locus tag
seq_index = headers.index("Sequence") # Get the gene name
it = 0
for i, item in enumerate(self.selected_table_items): # Loop through all the items in the View Targets table
if (i+1) % num_cols == 0:
tmp_list.append(item.text())
tmp_list.append(gene_name)
output_data.write(delim.join(tmp_list)+"\n")
tmp_list.clear()
it = 0 # Reset iterator
elif it == seq_index:
tmp_list.append(item.text())
tmp_list.append(self.leading_seq.text().strip() + item.text() + self.trailing_seq.text().strip()) #5' Leader + gRNA + 3' Trailer
it += 1
else:
tmp_list.append(item.text())
it += 1
elif self.window in ["mt", "pa"]: #If the user is exporting data from multitargeting
seq_index = headers.index("Consensus Sequence")
it = 0
for i, item in enumerate(self.selected_table_items): # Loop through all the items in the View Targets table
if (i+1) % num_cols == 0:
tmp_list.append(item.text())
output_data.write(str(delim.join(tmp_list))+"\n")
tmp_list.clear()
it = 0 # Reset iterator
elif it == seq_index:
tmp_list.append(item.text())
tmp_list.append(self.leading_seq.text().strip() + item.text() + self.trailing_seq.text().strip()) #5' Leader + gRNA + 3' Trailer
it += 1
else:
tmp_list.append(item.text())
it += 1
else: #If the user is exporting data from View Targets but is not using Feature search
seq_index = headers.index("Sequence") # Get the gene name
it = 0
for i, item in enumerate(self.selected_table_items): # Loop through all the items in the View Targets table
if (i+1) % num_cols == 0:
tmp_list.append(item.text())
output_data.write(delim.join(tmp_list)+"\n")
tmp_list.clear()
it = 0 # Reset iterator
elif it == seq_index:
tmp_list.append(item.text())
tmp_list.append(self.leading_seq.text().strip() + item.text() + self.trailing_seq.text().strip()) #5' Leader + gRNA + 3' Trailer
it += 1
else:
tmp_list.append(item.text())
it += 1
output_data.close()
# catch the permission exception
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
# catch any other exception
except Exception as e:
print(e)
return
""" Print "finished" message """
msgBox = QtWidgets.QMessageBox()
msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
msgBox.setIcon(QtWidgets.QMessageBox.Icon.Information)
msgBox.setWindowTitle("Export Complete")
msgBox.setText("Export to %s was successful." % full_path)
msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
msgBox.exec()
# close the window
self.cancel_function()
except Exception as e:
logger.critical("Error in export_function() in export_tool.")
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)
# Resets everything to the init funciton
# then closes the window
def cancel_function(self):
try:
if platform.system() == "Windows":
self.fileLocation_line_edit.setText(GlobalSettings.CSPR_DB + "\\")
else:
self.fileLocation_line_edit.setText(GlobalSettings.CSPR_DB + "/")
self.filename_line_edit.setText("")
self.location = ""
self.hide()
except Exception as e:
logger.critical("Error in cancel_function() in export_tool.")
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 for folder function
# allows user to browse for a folder where to store the CSV file
def browseForFolder(self):
try:
# 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
if platform.system() == "Windows":
self.fileLocation_line_edit.setText(mydir + "\\")
self.location = mydir + "\\"
else:
self.fileLocation_line_edit.setText(mydir + "/")
self.location = mydir + "/"
except Exception as e:
logger.critical("Error in browseForFolder() in export_tool.")
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)