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populationAnalysis.py
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from PyQt5 import QtWidgets, Qt, QtGui, QtCore, uic
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg
from matplotlib.figure import Figure
import GlobalSettings
import os
import Algorithms
import numpy as np
from PyQt5.QtWidgets import *
import gzip
import sqlite3
import itertools
import matplotlib.patches as patches
import mplcursors
import copy
import traceback
import math
#global logger
logger = GlobalSettings.logger
#population analysis class
class Pop_Analysis(QtWidgets.QMainWindow):
#init class
def __init__(self):
try:
super(Pop_Analysis, self).__init__()
uic.loadUi(GlobalSettings.appdir + 'pop.ui', self)
self.setWindowIcon(Qt.QIcon(GlobalSettings.appdir + "cas9image.ico"))
self.goBackButton.clicked.connect(self.go_back)
self.analyze_button.clicked.connect(self.pre_analyze)
self.clear_Button.clicked.connect(self.clear)
self.export_button.clicked.connect(self.export_tool)
self.sq = Algorithms.SeqTranslate()
self.ref_para_list = list()
self.mode = 0
self.find_locs_button.clicked.connect(self.find_locations)
self.clear_loc_button.clicked.connect(self.clear_loc_table)
self.names = []
self.names_venn = []
""" Colormap Graph initialization """
self.colormap_layout = QtWidgets.QVBoxLayout()
self.colormap_layout.setContentsMargins(0,0,0,0)
self.colormap_canvas = MplCanvas(self) ###Initialize new Canvas
groupbox_style = """
QGroupBox:title{subcontrol-origin: margin;
left: 10px;
padding: 0 5px 0 15px;}
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.groupBox_2.setStyleSheet(groupbox_style.replace("groupBox","groupBox_2"))
#organism table
self.org_Table.setColumnCount(1)
self.org_Table.setShowGrid(False)
self.org_Table.setHorizontalHeaderLabels(["Organism"])
self.org_Table.horizontalHeader().setSectionsClickable(True)
self.org_Table.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.org_Table.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows)
self.org_Table.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.org_Table.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
#self.org_Table.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents)
#top-right table
self.table2.setColumnCount(9)
self.table2.setShowGrid(False)
self.table2.setHorizontalHeaderLabels(["Seed","% Coverage","Total Repeats","Avg. Repeats/Scaffold", "Consensus Sequence", "% Consensus", "Score","PAM", "Strand"])
self.table2.horizontalHeader().setSectionsClickable(True)
self.table2.horizontalHeader().sectionClicked.connect(self.table2_sorting)
self.table2.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
self.table2.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents)
self.table2.setSelectionBehavior(QtWidgets.QTableView.SelectRows)
self.table2.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
self.table2.resizeColumnsToContents()
# Finder table
self.loc_finder_table.setColumnCount(5)
self.loc_finder_table.setShowGrid(False)
self.loc_finder_table.setHorizontalHeaderLabels(["Seed ID", "Sequence", "Organism", "Scaffold", "Location"])
self.loc_finder_table.horizontalHeader().setSectionsClickable(True)
self.loc_finder_table.horizontalHeader().sectionClicked.connect(self.loc_table_sorter)
self.loc_finder_table.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeToContents)
self.loc_finder_table.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers)
#self.loc_finder_table.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents)
# self.loc_finder_table.setSelectionBehavior(QtWidgets.QTableView.SelectRows)
# self.loc_finder_table.setSelectionMode(QtWidgets.QAbstractItemView.MultiSelection)
self.loc_finder_table.resizeColumnsToContents()
#custom seed search
self.query_seed_button.clicked.connect(self.custom_seed_search)
self.total_org_number = 0
self.switcher_table2 = [1, 1, 1, 1, 1, 1, 1, 1,
1] # for keeping track of where we are in the sorting clicking for each column
self.switcher_loc_table = [1, 1, 1, 1, 1]
#Initialize variables
self.index_to_cspr = {}
self.index_to_db = {}
self.name_to_db = {}
self.cspr_files = []
self.db_files = []
self.Endos = {}
self.seeds = []
self.loading_window = loading_window()
#scale UI
self.first_show = True
self.scaleUI()
except Exception as e:
logger.critical("Error initializing population analysis.")
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 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()
self.dpi = dpi
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.title.setStyleSheet("font: bold " + str(fontSize) + "pt 'Arial';")
self.groupBox.setMaximumWidth(int(width * 0.3))
self.adjustSize()
currentWidth = self.size().width()
currentHeight = self.size().height()
# window scaling
# 1920x1080 => 1150x650
scaledWidth = int((width * 1150) / 1920)
scaledHeight = int((height * 650) / 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 population analysis.")
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 population analysis.")
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 shared seed table to csv function
def export_tool(self):
try:
select_items = self.table2.selectedItems()
if len(select_items) <= 0:
msgBox = QtWidgets.QMessageBox()
msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
msgBox.setWindowTitle("Nothing Selected")
msgBox.setText("No targets were highlighted. Please highlight the targets you want to be exported to a CSV File!")
msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
msgBox.exec()
return
GlobalSettings.mainWindow.export_tool_window.launch(select_items,"pa")
except Exception as e:
logger.critical("Error in export_tool() in population analysis.")
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 calls the popParser function and fills all the tables
def pre_analyze(self):
try:
#clear saved filenames
self.cspr_files = []
self.db_files = []
self.rows = []
#get selected indexes
selected_indexes = self.org_Table.selectionModel().selectedRows()
# error check
if len(selected_indexes) == 0:
msgBox = QtWidgets.QMessageBox()
msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
msgBox.setWindowTitle("Error")
msgBox.setText("Please select CSPR file(s) for analysis.")
msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
msgBox.exec()
return
#get cspr and db filenames
for index in sorted(selected_indexes):
self.rows.append(index.row() + 1)
self.cspr_files.append(self.index_to_cspr[index.row()])
self.db_files.append(self.index_to_db[index.row()])
self.get_org_names()
self.fill_data()
except Exception as e:
logger.critical("Error in pre_analyze() in population analysis.")
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 calling get_data()
def launch(self):
try:
self.get_data()
except Exception as e:
logger.critical("Error in launch() in population analysis.")
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)
#responsible for calling all loading/analysis functions for loading the shared seeds table and generating the heatmap based on selected organisms
def get_data(self):
try:
self.fillEndo()
except Exception as e:
logger.critical("Error in get_data() in population analysis.")
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 opens CASPERinfo and builds the dropdown menu of selectable endonucleases
def fillEndo(self):
try:
try:
self.endoBox.currentIndexChanged.disconnect()
except:
pass
self.Endos = {}
self.endoBox.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(";")
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]
default_five_length = line_tokened[2]
default_seed_length = line_tokened[3]
default_three_length = line_tokened[4]
self.Endos[endo + " PAM: " + p_pam] = (endo, p_pam, default_five_length, default_seed_length, default_three_length)
break
f.close()
self.endoBox.addItems(self.Endos.keys())
self.endoBox.currentIndexChanged.connect(self.change_endo)
self.change_endo()
except Exception as e:
logger.critical("Error in fillEndo() in population analysis.")
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 updating the organism options based on the endo selected
def change_endo(self):
try:
self.org_Table.clearContents()
self.org_Table.setRowCount(0)
onlyfiles = [f for f in os.listdir(GlobalSettings.CSPR_DB) if os.path.isfile(os.path.join(GlobalSettings.CSPR_DB, f))]
index = 0
for file in onlyfiles:
if file.find('.cspr') != -1:
endo = file[file.rfind('_') + 1:file.find('.cspr')]
if endo == self.Endos[self.endoBox.currentText()][0]:
# increase row count
self.org_Table.setRowCount(index + 1)
# open .cspr file and get genome name
f = open(file, 'r')
line = f.readline()
f.close()
line = str(line)
line = line.split(":")[-1].strip()
orgName = line
# add genome name to table
tabWidget = QtWidgets.QTableWidgetItem(orgName)
tabWidget.setTextAlignment(QtCore.Qt.AlignVCenter)
self.org_Table.setItem(index, 0, tabWidget)
# store cspr and db file information for later
self.index_to_cspr[index] = file
db_file = file.replace(".cspr", "")
db_file += "_repeats.db"
self.index_to_db[index] = db_file
# incrase row index
index += 1
if index == 0:
self.org_Table.clearContents()
self.org_Table.setRowCount(0)
self.org_Table.resizeColumnsToContents()
except Exception as e:
logger.critical("Error in change_endo() in population analysis.")
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)
#fills shared seed table with data from analysis
def fill_data(self):
try:
#update progress bar
self.loading_window.loading_bar.setValue(5)
self.loading_window.centerUI()
self.loading_window.show()
QtCore.QCoreApplication.processEvents()
#prep table
self.total_org_number = len(self.cspr_files)
self.table2.setRowCount(0)
self.loading_window.loading_bar.setValue(10)
index = 0
self.seeds = self.get_shared_seeds(self.db_files, True)
try:
os.remove(GlobalSettings.appdir + "temp_join.db")
except:
pass
no_seeds = False
if(len(self.seeds) == 0):
no_seeds = True
#QtCore.QCoreApplication.processEvents()
#retrieve data on shared seeds
if no_seeds == False:
increase_val = float(15 / len(self.seeds))
running_val = self.loading_window.loading_bar.value()
self.loading_window.info_label.setText("Parsing Seed Data")
self.counts = []
for seed in self.seeds:
# increase row count
self.table2.setRowCount(index + 1)
# push seed to table
table_seed = QtWidgets.QTableWidgetItem()
table_seed.setData(QtCore.Qt.EditRole, seed)
table_seed.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 0, table_seed)
total_count = 0
org_count = 0
threes = []
fives = []
scores = []
pams = []
locs = []
for db_file in self.db_files:
conn = sqlite3.connect(db_file)
c = conn.cursor()
data = c.execute("SELECT count, three, five, pam, score, location FROM repeats WHERE seed = ? ",(seed,)).fetchone()
if data != None:
data = list(data)
org_count += 1
total_count += int(data[0])
threes += data[1].split(",")
fives += data[2].split(",")
pams += data[3].split(",")
scores += data[4].split(",")
locs += data[5].split(",")
self.counts.append(total_count)
if len(threes) < len(fives):
for i in range(len(fives) - len(threes)):
threes.append('')
elif len(fives) < len(threes):
for i in range(len(threes) - len(fives)):
fives.append('')
majority_index = 0
three_prime, five_prime, both_prime = False, False, False
if threes[0] == '':
majority = max(set(fives), key=fives.count)
majority_index = fives.index(majority)
five_prime = True
elif fives[0] == '':
majority = max(set(threes), key=threes.count)
majority_index = threes.index(majority)
three_prime = True
else:
#account for both 3 and 5 present
threes_and_fives = []
for i in range(len(threes)):
threes_and_fives.append(threes[i] + fives[i])
majority = max(set(threes_and_fives), key=threes_and_fives.count)
majority_index = threes_and_fives.index(majority)
both_prime = True
# push percent coverage
perc_cov = QtWidgets.QTableWidgetItem()
coverage = (org_count / len(self.db_files)) * 100
coverage = float("%.2f" % coverage)
perc_cov.setData(QtCore.Qt.EditRole, coverage)
perc_cov.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 1, perc_cov)
# push total count
table_count = QtWidgets.QTableWidgetItem()
table_count.setData(QtCore.Qt.EditRole, total_count)
table_count.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 2, table_count)
# push avg repeat
avg_rep = QtWidgets.QTableWidgetItem()
avg_rep_per_scaff = total_count / org_count
avg_rep_per_scaff = float("%.2f" % avg_rep_per_scaff)
avg_rep.setData(QtCore.Qt.EditRole, avg_rep_per_scaff)
avg_rep.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 3, avg_rep)
# push seq
seq = QtWidgets.QTableWidgetItem()
seq.setData(QtCore.Qt.EditRole, fives[majority_index] + seed + threes[majority_index])
seq.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 4, seq)
# push percent consensus
perc_cons = QtWidgets.QTableWidgetItem()
percent_consensus = 0
if five_prime == True:
percent_consensus = (fives.count(fives[majority_index]) / len(fives)) * 100
elif three_prime == True:
percent_consensus = (threes.count(threes[majority_index]) / len(threes)) * 100
elif both_prime:
percent_consensus = (threes_and_fives.count(threes_and_fives[majority_index]) / len(threes_and_fives)) * 100
percent_consensus = float("%.2f" % percent_consensus)
perc_cons.setData(QtCore.Qt.EditRole, percent_consensus)
perc_cons.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 5, perc_cons)
# push score
score = QtWidgets.QTableWidgetItem()
score.setData(QtCore.Qt.EditRole, scores[majority_index])
score.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 6, score)
# push PAM
pam = QtWidgets.QTableWidgetItem()
pam.setData(QtCore.Qt.EditRole, pams[majority_index])
pam.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 7, pam)
# push strand
strand_val = ""
if int(locs[majority_index]) < 0:
strand_val = "-"
else:
strand_val = "+"
strand = QtWidgets.QTableWidgetItem()
strand.setData(QtCore.Qt.EditRole, strand_val)
strand.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 8, strand)
index += 1
running_val += increase_val
self.loading_window.loading_bar.setValue(int(running_val))
self.table2.resizeColumnsToContents()
self.loading_window.loading_bar.setValue(25)
if len(self.db_files) > 1:
self.plot_3D_graph()
else:
self.colormap_canvas.figure.set_visible(False)
self.loading_window.loading_bar.setValue(100)
self.loading_window.hide()
QtCore.QCoreApplication.processEvents()
except Exception as e:
logger.critical("Error in fill_data() in population analysis.")
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)
#function to allow user to search for a specific seed amongst the organisms analyzed
def custom_seed_search(self):
try:
seeds = str(self.seed_input.text())
seeds = seeds.replace(" ","")
seeds = seeds.upper()
seeds = seeds.split(",")
if len(seeds) == 1:
if seeds[0] == "":
self.pre_analyze()
return
# update progress bar
self.loading_window.loading_bar.setValue(5)
self.loading_window.show()
QtCore.QCoreApplication.processEvents()
# prep table
self.total_org_number = len(self.cspr_files)
self.loading_window.loading_bar.setValue(10)
index = 0
if (len(seeds) == 0):
self.loading_window.hide()
return
if len(self.seeds) == 0:
self.loading_window.hide()
msgBox = QtWidgets.QMessageBox()
msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
msgBox.setWindowTitle("Error")
msgBox.setText("No analysis has been run to be able to search for a specific seed.")
msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
msgBox.exec()
return
increase_val = float(15 / len(self.seeds))
running_val = self.loading_window.loading_bar.value()
self.loading_window.info_label.setText("Parsing Seed Data")
# QtCore.QCoreApplication.processEvents()
self.table2.setRowCount(0)
# retrieve data on shared seeds
self.counts = []
for seed in seeds:
total_count = 0
org_count = 0
threes = []
fives = []
scores = []
pams = []
locs = []
none_data = True
for db_file in self.db_files:
conn = sqlite3.connect(db_file)
c = conn.cursor()
data = c.execute("SELECT count, three, five, pam, score, location FROM repeats WHERE seed = ?",
(seed,)).fetchone()
if data != None:
none_data = False
data = list(data)
org_count += 1
total_count += int(data[0])
threes += data[1].split(",")
fives += data[2].split(",")
pams += data[3].split(",")
scores += data[4].split(",")
locs += data[5].split(",")
if none_data == True:
self.loading_window.hide()
msgBox = QtWidgets.QMessageBox()
msgBox.setStyleSheet("font: " + str(self.fontSize) + "pt 'Arial'")
msgBox.setIcon(QtWidgets.QMessageBox.Icon.Critical)
msgBox.setWindowTitle("Seed Error")
msgBox.setText(seed + " : No such seed exists in the repeats section of any organism selected.")
msgBox.addButton(QtWidgets.QMessageBox.StandardButton.Ok)
msgBox.exec()
return
else:
# increase row count
self.table2.setRowCount(index + 1)
# push seed to table
table_seed = QtWidgets.QTableWidgetItem()
table_seed.setData(QtCore.Qt.EditRole, seed)
table_seed.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 0, table_seed)
self.counts.append(total_count)
if len(threes) < len(fives):
for i in range(len(fives) - len(threes)):
threes.append('')
elif len(fives) < len(threes):
for i in range(len(threes) - len(fives)):
fives.append('')
majority_index = 0
three_prime, five_prime, both_prime = False, False, False
if threes[0] == '':
majority = max(set(fives), key=fives.count)
majority_index = fives.index(majority)
five_prime = True
elif fives[0] == '':
majority = max(set(threes), key=threes.count)
majority_index = threes.index(majority)
three_prime = True
else:
# account for both 3 and 5 present
threes_and_fives = []
for i in range(len(threes)):
threes_and_fives.append(threes[i] + fives[i])
majority = max(set(threes_and_fives), key=threes_and_fives.count)
majority_index = threes_and_fives.index(majority)
both_prime = True
# push percent coverage
perc_cov = QtWidgets.QTableWidgetItem()
coverage = (org_count / len(self.db_files)) * 100
coverage = float("%.2f" % coverage)
perc_cov.setData(QtCore.Qt.EditRole, coverage)
perc_cov.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 1, perc_cov)
# push total count
table_count = QtWidgets.QTableWidgetItem()
table_count.setData(QtCore.Qt.EditRole, total_count)
table_count.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 2, table_count)
# push avg repeat
avg_rep = QtWidgets.QTableWidgetItem()
avg_rep_per_scaff = total_count / org_count
avg_rep_per_scaff = float("%.2f" % avg_rep_per_scaff)
avg_rep.setData(QtCore.Qt.EditRole, avg_rep_per_scaff)
avg_rep.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 3, avg_rep)
# push seq
seq = QtWidgets.QTableWidgetItem()
seq.setData(QtCore.Qt.EditRole, fives[majority_index] + seed + threes[majority_index])
seq.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 4, seq)
# push percent consensus
perc_cons = QtWidgets.QTableWidgetItem()
percent_consensus = 0
if five_prime == True:
percent_consensus = (fives.count(fives[majority_index]) / len(fives)) * 100
elif three_prime == True:
percent_consensus = (threes.count(threes[majority_index]) / len(threes)) * 100
elif both_prime:
percent_consensus = (threes_and_fives.count(threes_and_fives[majority_index]) / len(threes_and_fives)) * 100
percent_consensus = float("%.2f" % percent_consensus)
perc_cons.setData(QtCore.Qt.EditRole, percent_consensus)
perc_cons.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 5, perc_cons)
# push score
score = QtWidgets.QTableWidgetItem()
score.setData(QtCore.Qt.EditRole, scores[majority_index])
score.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 6, score)
# push PAM
pam = QtWidgets.QTableWidgetItem()
pam.setData(QtCore.Qt.EditRole, pams[majority_index])
pam.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 7, pam)
# push strand
strand_val = ""
if int(locs[majority_index]) < 0:
strand_val = "-"
else:
strand_val = "+"
strand = QtWidgets.QTableWidgetItem()
strand.setData(QtCore.Qt.EditRole, strand_val)
strand.setTextAlignment(QtCore.Qt.AlignHCenter | QtCore.Qt.AlignVCenter)
self.table2.setItem(index, 8, strand)
index += 1
running_val += increase_val
self.loading_window.loading_bar.setValue(int(running_val))
self.table2.resizeColumnsToContents()
self.loading_window.hide()
QtCore.QCoreApplication.processEvents()
except Exception as e:
logger.critical("Error in custom_seed_search() in population analysis.")
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)
#db_files is an array of database files for the organisms that will be looked at for shared seeds
def get_shared_seeds(self, db_files, limit=False):
try:
#vars
aliases = []
#get db attachment aliases
for i in range(1, len(db_files) + 1):
aliases.append("main" + str(i))
#memory connections for inner join on db files to hold what seeds are shared
new_conn = sqlite3.connect(GlobalSettings.appdir + "temp_join.db")
new_c = new_conn.cursor()
new_c.execute("PRAGMA synchronous = OFF;")
new_c.execute("PRAGMA journal_mode = OFF;")
new_c.execute("PRAGMA locking_mode = EXCLUSIVE;")
new_c.execute("DROP TABLE IF EXISTS repeats;")
new_c.execute("VACUUM;")
new_c.execute("DROP TABLE IF EXISTS join_results;")
new_c.execute("CREATE table join_results (seed TEXT PRIMARY KEY);")
#attach each db file with an alias
for i in range(len(db_files)):
new_c.execute("ATTACH DATABASE '" + db_files[i] + "' AS " + aliases[i] + ";")
# start transaction
new_c.execute("BEGIN TRANSACTION;")
sql_inner_join = "INSERT into main.join_results select main1.repeats.seed from main1.repeats "
for i in range(len(aliases[:-1])):
sql_inner_join += "inner join " + aliases[i + 1] + ".repeats on "
sql_inner_join += aliases[i] + ".repeats.seed = " + aliases[i + 1] + ".repeats.seed "
#execute inner join
new_c.execute(sql_inner_join)
#get shared data
if limit == False:
shared_seeds = new_c.execute("select count(*) from join_results").fetchall()
return shared_seeds
else:
shared_seeds = new_c.execute("select * from join_results limit 0,1000").fetchall()
#end transaction
new_c.execute("END TRANSACTION;")
#close memory db
new_c.close()
new_conn.close()
#parse shared seeds into self.seeds
seeds = []
for tup in shared_seeds:
seeds.append(tup[0])
return seeds
except Exception as e:
logger.critical("Error in get_shared_seeds() in population analysis.")
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)
#get the names of organism in current directory
def get_org_names(self):
try:
self.org_names = {}
for file in self.cspr_files:
with open(file, "r") as f:
line = f.readline()
buf = str(line)
buf = buf.strip()
org_name = buf.replace("GENOME: ", "")
line = f.readline()
buf = str(line)
kstats = buf.replace("KARYSTATS: ", "")
kstats = kstats.split(",")
self.org_names[org_name] = len(kstats) - 1
except Exception as e:
logger.critical("Error in get_org_names() in population analysis.")
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)
#plot the heatmap graph
def plot_3D_graph(self):
try:
for i in reversed(range(self.colormap_layout.count())): ### Clear out old widges in layout
self.colormap_layout.itemAt(i).widget().setParent(None)
self.colormap_canvas = MplCanvas(self, width=5, height=3, dpi=self.dpi) ###Initialize new Canvas
self.colormap_layout.addWidget(self.colormap_canvas) ### Add canvas to colormap layout
self.colormap_figure.setLayout(self.colormap_layout) ### Add colormap layout to colormap plot widget
# self.colormap_canvas.axes.clear()
# try:
# self.colormap_canvas.cbar.remove()
# except:
# None
# self.colormap_canvas.figure.set_visible(True)
rows, cols = (self.total_org_number, self.total_org_number)
arr = [[0 for i in range(cols)] for j in range(rows)]
self.names = list(self.org_names.keys())
for pair in list(itertools.combinations(self.db_files, 2)):
shared_seeds = list(self.get_shared_seeds(list(pair), False)[0])[0]
arr[self.db_files.index(pair[0])][self.db_files.index(pair[1])] += int(shared_seeds)
arr[self.db_files.index(pair[1])][self.db_files.index(pair[0])] += int(shared_seeds)
for i in range(len(arr)):
conn = sqlite3.connect(self.db_files[i])
c = conn.cursor()
arr[i][i] = int(list(c.execute("select count(*) from repeats;").fetchall()[0])[0])
c.close()
conn.close()
labels = copy.deepcopy(arr)
for i in range(len(arr)):
arr[i][i] = 0
ax = self.colormap_canvas.axes