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GUI.py
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GUI.py
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# -*- coding: utf-8 -*-
import logging
import os
import sys
import webbrowser
from multiprocessing import freeze_support
from time import sleep
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5 import __file__ as qt_file
from PyQt5.QtWidgets import QMainWindow, QFileDialog
import pageant as main
main.plt.switch_backend('Agg')
if main.platform == 'Darwin':
os.chdir(main.raw_dir)
default_font_size = 10 if main.platform == 'Linux' else 11
y_offset = 0 if main.platform == 'Windows' else 10
QtGui.QGuiApplication.addLibraryPath(os.path.join(os.path.dirname(qt_file), 'Qt', 'plugins', 'platforms'))
QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling)
default_config = {value: key[value] for key in main.load_config().values() for value in key}
default_config.update({
'name': 'HG001',
'input_file': './personal_genome/HG001.vcf.gz',
'config_file': './bin/config.ini',
'quan_data': './algorithm/Quantitative',
'qual_data': './algorithm/Qualitative',
'quan_ref': './population_genome',
'qual_ref': './population_genome',
# 'qr_snps_txt': './personal_genome/fingerprint_snps.txt',
'maf_ref': './population_genome/g1k_ps.vcf.gz',
'ps_ref': './population_genome/g1k_ps.vcf.gz',
'concord_ref': './personal_genome/concordance.vcf.gz'
})
def index_to_sep(ind: int) -> str:
return {0: '\t', 1: ',', 2: ' '}[ind]
def get_ethnicity_list(samples_file: str) -> main.List[str]:
samples_info = '.'.join(samples_file.split('.')[:-1] + ['samples'])
if os.path.isfile(samples_info):
ethnicities = set([])
with open(samples_info) as f:
f.readline()
for line in f:
ethnicities.add(line.strip().split('\t')[-1])
return sorted(ethnicities)
else:
return []
def set_ethnicity_item(ethnicities: main.List[str], combobox: QtWidgets.QComboBox):
combobox.clear()
if ethnicities:
combobox.addItems(['All'] + ethnicities)
combobox.setCurrentIndex(4)
else:
combobox.setPlaceholderText('---No ethnicity is founded !---')
combobox.addItem('All')
combobox.setCurrentIndex(-1)
# def umap(*args, **kwargs):
# main.get_plink_dir(os.path.join(os.getcwd(), 'bin'))
# main.ps_analyse(*args, **kwargs)
class GUIHandler(logging.Handler):
def __init__(self, connector: QtWidgets.QProgressDialog, progress_value, *args, **kwargs):
super().__init__(*args, **kwargs)
self.connector = connector
self.progress = progress_value
def emit(self, record):
msg = self.format(record)
if 'Progress of the analysis: ' in msg:
self.progress.value = float(msg.split(': ')[-1].replace('%', ''))
elif 'start' in msg:
self.connector.setLabelText(msg)
class MyThread(QtCore.QThread):
def __init__(self, handler, parameters: dict):
super().__init__()
self.statue = False
self.res = 'Analysis failed to start.'
self.parameters = parameters
self.handler = handler
self.setStackSize(10240000)
main.gui_log_setup(self.handler)
def run(self):
sleep(0.5)
try:
self.res = main.main(**self.parameters)
except Exception as e:
self.res = str(e).capitalize()
else:
self.statue = True
finally:
self.quit()
main.gui_log_remove(self.handler)
# class API_Thread(QtCore.QThread):
# def __init__(self, func: main.Callable, *args,
# end_: str = 'Finish! Result has been saved in the working directory.', **kwargs):
# super().__init__()
# self.statue = False
# self.res = 'Analysis failed to start.'
# self.func = func
# self.args = args
# self.kwargs = kwargs
# self.end = end_
# self.setStackSize(10240000)
#
# def run(self):
# sleep(0.5)
# try:
# self.func(*self.args, **self.kwargs)
# except Exception as e:
# self.res = str(e).capitalize()
# else:
# self.statue = True
# self.res = self.end
# finally:
# self.quit()
class ProgressValue:
def __init__(self):
self.value = 0
class ProgressNow:
def __init__(self, inter: int):
self.now_value = 0
self.inter = 1000 / inter
def value(self):
return int(self.now_value // self.inter)
def add(self):
self.now_value += 1
def set(self, value: int):
self.now_value = value * self.inter
class Ui_PAGEANT(object):
def setupUi(self, PAGEANT):
PAGEANT.setObjectName("PAGEANT")
PAGEANT.setWindowModality(QtCore.Qt.WindowModal)
PAGEANT.setEnabled(True)
PAGEANT.resize(600, 480)
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Preferred,
QtWidgets.QSizePolicy.Preferred)
sizePolicy.setHorizontalStretch(60)
sizePolicy.setVerticalStretch(48)
sizePolicy.setHeightForWidth(PAGEANT.sizePolicy().hasHeightForWidth())
PAGEANT.setSizePolicy(sizePolicy)
PAGEANT.setMinimumSize(QtCore.QSize(600, 480))
PAGEANT.setMaximumSize(QtCore.QSize(600, 480))
font = QtGui.QFont()
font.setFamily("Calibri")
font.setPointSize(default_font_size)
font.setBold(True)
font1 = QtGui.QFont()
font1.setFamily("Calibri")
font1.setPointSize(default_font_size - 1)
font1.setBold(False)
font2 = QtGui.QFont()
font2.setFamily("Calibri")
font2.setPointSize(default_font_size)
font2.setBold(False)
font2.setKerning(True)
font2.setStyleStrategy(QtGui.QFont.PreferDefault)
font3 = QtGui.QFont()
font3.setFamily("Calibri")
font3.setPointSize(default_font_size)
font3.setBold(False)
font4 = QtGui.QFont()
font4.setFamily("Calibri")
font4.setPointSize(default_font_size)
font4.setBold(True)
font4.setKerning(True)
font4.setStyleStrategy(QtGui.QFont.PreferDefault)
PAGEANT.setFont(font)
PAGEANT.setAutoFillBackground(False)
self.MainWindow = QtWidgets.QWidget(PAGEANT)
self.MainWindow.setFont(font)
self.MainWindow.setObjectName("MainWindow")
self.Function = QtWidgets.QTabWidget(self.MainWindow)
self.Function.setGeometry(QtCore.QRect(15, 10, 571, 461))
sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed)
sizePolicy.setHorizontalStretch(0)
sizePolicy.setVerticalStretch(0)
sizePolicy.setHeightForWidth(self.Function.sizePolicy().hasHeightForWidth())
self.Function.setSizePolicy(sizePolicy)
self.Function.setMinimumSize(QtCore.QSize(0, 0))
self.Function.setFont(font)
self.Function.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
self.Function.setStyleSheet("")
self.Function.setIconSize(QtCore.QSize(25, 20))
self.Function.setDocumentMode(False)
self.Function.setTabsClosable(False)
self.Function.setMovable(False)
self.Function.setTabBarAutoHide(False)
self.Function.setObjectName("Function")
self.Basic = QtWidgets.QWidget()
self.Basic.setFont(font)
self.Basic.setObjectName("Basic")
self.i_vcf = QtWidgets.QLineEdit(self.Basic)
self.i_vcf.setGeometry(QtCore.QRect(79, 141, 365, 25))
self.i_vcf.setFont(font1)
self.i_vcf.setObjectName("i_vcf")
self.b_analyze = QtWidgets.QPushButton(self.Basic)
self.b_analyze.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_analyze.setFont(font)
self.b_analyze.setObjectName("b_analyze")
self.s_vcf = QtWidgets.QToolButton(self.Basic)
self.s_vcf.setGeometry(QtCore.QRect(440, 140, 41, 27))
self.s_vcf.setFont(font1)
self.s_vcf.setObjectName("s_vcf")
self.l_vcf = QtWidgets.QLabel(self.Basic)
self.l_vcf.setGeometry(QtCore.QRect(40, 110, 121, 20))
self.l_vcf.setFont(font)
self.l_vcf.setObjectName("l_vcf")
self.l_output = QtWidgets.QLabel(self.Basic)
self.l_output.setGeometry(QtCore.QRect(40, 290, 171, 20))
self.l_output.setFont(font)
self.l_output.setObjectName("l_output")
self.i_output = QtWidgets.QLineEdit(self.Basic)
self.i_output.setGeometry(QtCore.QRect(79, 321, 401, 25))
self.i_output.setFont(font1)
self.i_output.setObjectName("i_output")
self.s_output = QtWidgets.QToolButton(self.Basic)
self.s_output.setGeometry(QtCore.QRect(440, 320, 41, 27))
self.s_output.setFont(font1)
self.s_output.setObjectName("s_output")
self.l_name = QtWidgets.QLabel(self.Basic)
self.l_name.setGeometry(QtCore.QRect(40, 50, 61, 20))
self.l_name.setFont(font)
self.l_name.setObjectName("l_name")
self.i_name = QtWidgets.QLineEdit(self.Basic)
self.i_name.setGeometry(QtCore.QRect(100, 50, 121, 25))
self.i_name.setFont(font1)
self.i_name.setObjectName("i_name")
self.l_config = QtWidgets.QLabel(self.Basic)
self.l_config.setGeometry(QtCore.QRect(40, 200, 201, 25))
self.l_config.setFont(font)
self.l_config.setObjectName("l_config")
self.i_config = QtWidgets.QLineEdit(self.Basic)
self.i_config.setGeometry(QtCore.QRect(79, 231, 365, 25))
self.i_config.setFont(font1)
self.i_config.setObjectName("i_config")
self.s_config = QtWidgets.QToolButton(self.Basic)
self.s_config.setGeometry(QtCore.QRect(440, 230, 41, 27))
self.s_config.setFont(font1)
self.s_config.setObjectName("s_config")
self.i_output.raise_()
self.i_vcf.raise_()
self.b_analyze.raise_()
self.l_vcf.raise_()
self.l_output.raise_()
self.s_output.raise_()
self.l_name.raise_()
self.i_name.raise_()
self.s_vcf.raise_()
self.l_config.raise_()
self.i_config.raise_()
self.s_config.raise_()
self.Function.addTab(self.Basic, "")
self.QC = QtWidgets.QWidget()
self.QC.setFont(font)
self.QC.setStyleSheet("")
self.QC.setObjectName("QC")
self.c_sample_qc = QtWidgets.QGroupBox(self.QC)
self.c_sample_qc.setGeometry(QtCore.QRect(20, 20, 521, 351))
self.c_sample_qc.setFont(font)
self.c_sample_qc.setCheckable(True)
self.c_sample_qc.setChecked(True)
self.c_sample_qc.setObjectName("c_sample_qc")
# self.c_vep = QtWidgets.QCheckBox(self.c_sample_qc)
# self.c_vep.setGeometry(QtCore.QRect(30, 30, 451, 19))
#
# self.c_vep.setFont(font2)
# self.c_vep.setObjectName("c_vep")
self.PS = QtWidgets.QGroupBox(self.c_sample_qc)
self.PS.setEnabled(True)
self.PS.setGeometry(QtCore.QRect(10, 110, 501, 141))
self.PS.setFont(font)
self.PS.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
self.PS.setObjectName("PS")
self.l_ps_ref = QtWidgets.QLabel(self.PS)
self.l_ps_ref.setGeometry(QtCore.QRect(30, 20 + y_offset, 201, 25))
self.l_ps_ref.setFont(font3)
self.l_ps_ref.setObjectName("l_ps_ref")
self.i_ps_ref = QtWidgets.QLineEdit(self.PS)
self.i_ps_ref.setGeometry(QtCore.QRect(164, 21 + y_offset, 248, 25))
self.i_ps_ref.setFont(font1)
self.i_ps_ref.setObjectName("i_ps_ref")
self.s_ps_ref = QtWidgets.QToolButton(self.PS)
self.s_ps_ref.setGeometry(QtCore.QRect(410, 20 + y_offset, 41, 27))
self.s_ps_ref.setFont(font1)
self.s_ps_ref.setObjectName("s_ps_ref")
self.l_ps_pop = QtWidgets.QLabel(self.PS)
self.l_ps_pop.setGeometry(QtCore.QRect(30, 60 + y_offset, 181, 25))
self.l_ps_pop.setFont(font3)
self.l_ps_pop.setObjectName("l_ps_pop")
self.i_pop = QtWidgets.QLineEdit(self.PS)
self.i_pop.setGeometry(QtCore.QRect(370, 100 + y_offset, 81, 25))
self.i_pop.setFont(font1)
self.i_pop.setObjectName("i_pop")
self.l_pop = QtWidgets.QLabel(self.PS)
self.l_pop.setGeometry(QtCore.QRect(269, 100 + y_offset, 101, 25))
self.l_pop.setFont(font3)
self.l_pop.setObjectName("l_pop")
self.l_pop_sep = QtWidgets.QLabel(self.PS)
self.l_pop_sep.setGeometry(QtCore.QRect(30, 100 + y_offset, 61, 25))
self.l_pop_sep.setFont(font3)
self.l_pop_sep.setObjectName("l_pop_sep")
self.s_ps_pop = QtWidgets.QToolButton(self.PS)
self.s_ps_pop.setGeometry(QtCore.QRect(410, 60 + y_offset, 41, 27))
self.s_ps_pop.setFont(font1)
self.s_ps_pop.setObjectName("s_ps_pop")
self.i_ps_pop = QtWidgets.QLineEdit(self.PS)
self.i_ps_pop.setGeometry(QtCore.QRect(204, 61 + y_offset, 208, 25))
self.i_ps_pop.setFont(font1)
self.i_ps_pop.setObjectName("i_ps_pop")
self.i_pop_id = QtWidgets.QLineEdit(self.PS)
self.i_pop_id.setGeometry(QtCore.QRect(210, 101 + y_offset, 41, 25))
self.i_pop_id.setFont(font1)
self.i_pop_id.setObjectName("i_pop_id")
self.l_pop_id = QtWidgets.QLabel(self.PS)
self.l_pop_id.setGeometry(QtCore.QRect(160, 100 + y_offset, 61, 25))
self.l_pop_id.setFont(font3)
self.l_pop_id.setObjectName("l_pop_id")
self.s_pop_sep = QtWidgets.QComboBox(self.PS)
self.s_pop_sep.setGeometry(QtCore.QRect(90, 101 + y_offset, 51, 25))
self.s_pop_sep.setFont(font1)
self.s_pop_sep.setObjectName("s_pop_sep")
self.s_pop_sep.addItem("")
self.s_pop_sep.addItem("")
self.s_pop_sep.addItem("")
self.l_ps_ref.raise_()
self.i_ps_ref.raise_()
self.s_ps_ref.raise_()
self.l_ps_pop.raise_()
self.i_pop.raise_()
self.l_pop.raise_()
self.l_pop_sep.raise_()
self.i_ps_pop.raise_()
self.i_pop_id.raise_()
self.l_pop_id.raise_()
self.s_pop_sep.raise_()
self.s_ps_pop.raise_()
self.MAF = QtWidgets.QGroupBox(self.c_sample_qc)
self.MAF.setEnabled(True)
self.MAF.setGeometry(QtCore.QRect(10, 30, 501, 61))
self.MAF.setFont(font)
self.MAF.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
self.MAF.setObjectName("MAF")
self.l_maf_sample = QtWidgets.QLabel(self.MAF)
self.l_maf_sample.setGeometry(QtCore.QRect(30, 20 + y_offset, 201, 25))
self.l_maf_sample.setFont(font3)
self.l_maf_sample.setObjectName("l_maf_sample")
self.i_maf_sample = QtWidgets.QLineEdit(self.MAF)
self.i_maf_sample.setGeometry(QtCore.QRect(164, 21 + y_offset, 248, 25))
self.i_maf_sample.setFont(font1)
self.i_maf_sample.setObjectName("i_maf_sample")
self.s_maf_sample = QtWidgets.QToolButton(self.MAF)
self.s_maf_sample.setGeometry(QtCore.QRect(410, 20 + y_offset, 41, 27))
self.s_maf_sample.setFont(font1)
self.s_maf_sample.setObjectName("s_maf_sample")
self.Concordance = QtWidgets.QGroupBox(self.c_sample_qc)
self.Concordance.setEnabled(True)
self.Concordance.setGeometry(QtCore.QRect(10, 270, 501, 61))
self.Concordance.setFont(font)
self.Concordance.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
self.Concordance.setObjectName("Concordance")
self.l_concord_ref = QtWidgets.QLabel(self.Concordance)
self.l_concord_ref.setGeometry(QtCore.QRect(30, 20 + y_offset, 201, 25))
self.l_concord_ref.setFont(font3)
self.l_concord_ref.setObjectName("l_concord_ref")
self.i_concord_ref = QtWidgets.QLineEdit(self.Concordance)
self.i_concord_ref.setGeometry(QtCore.QRect(184, 21 + y_offset, 228, 25))
self.i_concord_ref.setFont(font1)
self.i_concord_ref.setObjectName("i_concord_ref")
self.s_concord_ref = QtWidgets.QToolButton(self.Concordance)
self.s_concord_ref.setGeometry(QtCore.QRect(410, 20 + y_offset, 41, 27))
self.s_concord_ref.setFont(font1)
self.s_concord_ref.setObjectName("s_concord_ref")
self.b_default_sample_qc = QtWidgets.QPushButton(self.QC)
self.b_default_sample_qc.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_default_sample_qc.setFont(font)
self.b_default_sample_qc.setObjectName("b_default_sample_qc")
self.Function.addTab(self.QC, "")
self.Qualitative = QtWidgets.QWidget()
self.Qualitative.setObjectName("Qualitative")
self.b_default_qual = QtWidgets.QPushButton(self.Qualitative)
self.b_default_qual.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_default_qual.setFont(font)
self.b_default_qual.setObjectName("b_default_qual")
self.g_qual = QtWidgets.QGroupBox(self.Qualitative)
self.g_qual.setGeometry(QtCore.QRect(20, 20, 521, 351))
self.g_qual.setObjectName("g_qual")
self.l_database_qual = QtWidgets.QLabel(self.g_qual)
self.l_database_qual.setGeometry(QtCore.QRect(30, 50, 201, 25))
self.l_database_qual.setFont(font)
self.l_database_qual.setObjectName("l_database_qual")
self.s_ref_qual = QtWidgets.QToolButton(self.g_qual)
self.s_ref_qual.setGeometry(QtCore.QRect(430, 170, 41, 27))
self.s_ref_qual.setFont(font1)
self.s_ref_qual.setObjectName("s_ref_qual")
self.i_database_qual = QtWidgets.QLineEdit(self.g_qual)
self.i_database_qual.setGeometry(QtCore.QRect(69, 81, 365, 25))
self.i_database_qual.setFont(font1)
self.i_database_qual.setObjectName("i_database_qual")
self.i_ref_qual = QtWidgets.QLineEdit(self.g_qual)
self.i_ref_qual.setGeometry(QtCore.QRect(69, 171, 365, 25))
self.i_ref_qual.setFont(font1)
self.i_ref_qual.setObjectName("i_ref_qual")
self.s_database_qual = QtWidgets.QToolButton(self.g_qual)
self.s_database_qual.setGeometry(QtCore.QRect(430, 80, 41, 27))
self.s_database_qual.setFont(font1)
self.s_database_qual.setObjectName("s_database_qual")
self.l_ref_qual = QtWidgets.QLabel(self.g_qual)
self.l_ref_qual.setGeometry(QtCore.QRect(30, 140, 201, 25))
self.l_ref_qual.setFont(font)
self.l_ref_qual.setObjectName("l_ref_qual")
self.l_qual_pop = QtWidgets.QLabel(self.g_qual)
self.l_qual_pop.setGeometry(QtCore.QRect(30, 230, 371, 25))
self.l_qual_pop.setFont(font)
self.l_qual_pop.setObjectName("l_quan_pop")
self.s_qual_pop = QtWidgets.QComboBox(self.g_qual)
self.s_qual_pop.setGeometry(QtCore.QRect(70, 260, 401, 25))
self.s_qual_pop.setFont(font1)
self.s_qual_pop.setObjectName("s_qual_pop")
self.g_qual.raise_()
self.b_default_qual.raise_()
self.Function.addTab(self.Qualitative, "")
self.Quantitative = QtWidgets.QWidget()
self.Quantitative.setFont(font)
self.Quantitative.setStyleSheet("")
self.Quantitative.setObjectName("Quantitative")
self.b_default_quan = QtWidgets.QPushButton(self.Quantitative)
self.b_default_quan.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_default_quan.setFont(font)
self.b_default_quan.setObjectName("b_default_quan")
self.g_quan = QtWidgets.QGroupBox(self.Quantitative)
self.g_quan.setGeometry(QtCore.QRect(20, 20, 521, 351))
self.g_quan.setObjectName("g_quan")
self.l_database_quan = QtWidgets.QLabel(self.g_quan)
self.l_database_quan.setGeometry(QtCore.QRect(30, 30, 201, 25))
self.l_database_quan.setFont(font)
self.l_database_quan.setObjectName("l_database_quan")
self.s_ref_quan = QtWidgets.QToolButton(self.g_quan)
self.s_ref_quan.setGeometry(QtCore.QRect(430, 130, 41, 27))
self.s_ref_quan.setFont(font1)
self.s_ref_quan.setObjectName("s_ref_quan")
self.i_database_quan = QtWidgets.QLineEdit(self.g_quan)
self.i_database_quan.setGeometry(QtCore.QRect(69, 61, 365, 25))
self.i_database_quan.setFont(font1)
self.i_database_quan.setObjectName("i_database_quan")
self.i_ref_quan = QtWidgets.QLineEdit(self.g_quan)
self.i_ref_quan.setGeometry(QtCore.QRect(69, 131, 365, 25))
self.i_ref_quan.setFont(font1)
self.i_ref_quan.setObjectName("i_ref_quan")
self.s_database_quan = QtWidgets.QToolButton(self.g_quan)
self.s_database_quan.setGeometry(QtCore.QRect(430, 60, 41, 27))
self.s_database_quan.setFont(font1)
self.s_database_quan.setObjectName("s_database_quan")
self.l_ref_quan = QtWidgets.QLabel(self.g_quan)
self.l_ref_quan.setGeometry(QtCore.QRect(30, 100, 201, 25))
self.l_ref_quan.setFont(font)
self.l_ref_quan.setObjectName("l_ref_quan")
self.l_quan_pop = QtWidgets.QLabel(self.g_quan)
self.l_quan_pop.setGeometry(QtCore.QRect(30, 170, 371, 25))
self.l_quan_pop.setFont(font)
self.l_quan_pop.setObjectName("l_quan_pop")
self.s_quan_pop = QtWidgets.QComboBox(self.g_quan)
self.s_quan_pop.setGeometry(QtCore.QRect(70, 200, 401, 25))
self.s_quan_pop.setFont(font1)
self.s_quan_pop.setObjectName("s_quan_pop")
self.PRS = QtWidgets.QGroupBox(self.g_quan)
self.PRS.setEnabled(True)
self.PRS.setGeometry(QtCore.QRect(30, 240, 461, 101))
self.PRS.setFont(font)
self.PRS.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
self.PRS.setObjectName("PRS")
self.l_p1 = QtWidgets.QLabel(self.PRS)
self.l_p1.setGeometry(QtCore.QRect(30, 30, 50, 25))
self.l_p1.setFont(font3)
self.l_p1.setObjectName("l_p1")
self.i_p1 = QtWidgets.QLineEdit(self.PRS)
self.i_p1.setGeometry(QtCore.QRect(80, 30, 121, 25))
self.i_p1.setFont(font1)
self.i_p1.setAccessibleDescription("")
self.i_p1.setObjectName("i_p1")
self.l_r2 = QtWidgets.QLabel(self.PRS)
self.l_r2.setGeometry(QtCore.QRect(260, 30, 50, 25))
self.l_r2.setFont(font3)
self.l_r2.setObjectName("l_r2")
self.i_r2 = QtWidgets.QLineEdit(self.PRS)
self.i_r2.setGeometry(QtCore.QRect(320, 30, 121, 25))
self.i_r2.setFont(font1)
self.i_r2.setObjectName("i_r2")
self.l_kb = QtWidgets.QLabel(self.PRS)
self.l_kb.setGeometry(QtCore.QRect(30, 60, 50, 25))
self.l_kb.setFont(font3)
self.l_kb.setObjectName("l_kb")
self.i_kb = QtWidgets.QLineEdit(self.PRS)
self.i_kb.setGeometry(QtCore.QRect(80, 60, 121, 25))
self.i_kb.setFont(font1)
self.i_kb.setObjectName("i_kb")
self.i_p_threshold = QtWidgets.QLineEdit(self.PRS)
self.i_p_threshold.setGeometry(QtCore.QRect(320, 60, 121, 25))
self.i_p_threshold.setFont(font1)
self.i_p_threshold.setObjectName("i_p_threshold")
self.l_p_threshold = QtWidgets.QLabel(self.PRS)
self.l_p_threshold.setGeometry(QtCore.QRect(230, 60, 101, 25))
self.l_p_threshold.setFont(font3)
self.l_p_threshold.setObjectName("l_p_threshold")
self.PRS.raise_()
self.Function.addTab(self.Quantitative, "")
self.Query_database = QtWidgets.QWidget()
self.Query_database.setFont(font)
self.Query_database.setObjectName("Query_database")
self.c_query_database = QtWidgets.QGroupBox(self.Query_database)
self.c_query_database.setGeometry(QtCore.QRect(30, 20, 501, 351))
self.c_query_database.setFont(font)
self.c_query_database.setCheckable(True)
self.c_query_database.setObjectName("c_query_database")
self.c_clinvar = QtWidgets.QCheckBox(self.c_query_database)
self.c_clinvar.setGeometry(QtCore.QRect(40, 60, 451, 19))
self.c_clinvar.setFont(font4)
self.c_clinvar.setChecked(True)
self.c_clinvar.setObjectName("c_clinvar")
self.c_pharmgkb = QtWidgets.QCheckBox(self.c_query_database)
self.c_pharmgkb.setGeometry(QtCore.QRect(40, 110, 451, 19))
self.c_pharmgkb.setFont(font4)
self.c_pharmgkb.setChecked(True)
self.c_pharmgkb.setObjectName("c_pharmgkb")
self.c_otherdb = QtWidgets.QGroupBox(self.c_query_database)
self.c_otherdb.setGeometry(QtCore.QRect(32, 160, 441, 141))
self.c_otherdb.setCheckable(True)
self.c_otherdb.setChecked(True)
self.c_otherdb.setObjectName("c_otherdb")
self.l_otherdb = QtWidgets.QLabel(self.c_otherdb)
self.l_otherdb.setGeometry(QtCore.QRect(27, 40, 201, 25))
self.l_otherdb.setFont(font3)
self.l_otherdb.setObjectName("l_otherdb")
self.i_otherdb = QtWidgets.QLineEdit(self.c_otherdb)
self.i_otherdb.setGeometry(QtCore.QRect(31, 81, 341, 25))
self.i_otherdb.setFont(font1)
self.i_otherdb.setObjectName("i_otherdb")
self.s_otherdb = QtWidgets.QToolButton(self.c_otherdb)
self.s_otherdb.setGeometry(QtCore.QRect(370, 80, 41, 27))
self.s_otherdb.setFont(font1)
self.s_otherdb.setObjectName("s_otherdb")
self.b_default_query_db = QtWidgets.QPushButton(self.Query_database)
self.b_default_query_db.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_default_query_db.setFont(font)
self.b_default_query_db.setObjectName("b_default_query_db")
self.Function.addTab(self.Query_database, "")
self.QR_code = QtWidgets.QWidget()
self.QR_code.setFont(font)
self.QR_code.setObjectName("QR_code")
self.c_qr_code = QtWidgets.QGroupBox(self.QR_code)
self.c_qr_code.setGeometry(QtCore.QRect(30, 20, 501, 351))
self.c_qr_code.setFont(font)
self.c_qr_code.setCheckable(True)
self.c_qr_code.setObjectName("c_qr_code")
self.l_qr_give = QtWidgets.QLabel(self.c_qr_code)
self.l_qr_give.setGeometry(QtCore.QRect(30, 180, 281, 25))
self.l_qr_give.setFont(font)
self.l_qr_give.setObjectName("l_qr_give")
self.i_qr_give = QtWidgets.QLineEdit(self.c_qr_code)
self.i_qr_give.setGeometry(QtCore.QRect(50, 211, 365, 25))
self.i_qr_give.setFont(font1)
self.i_qr_give.setObjectName("i_qr_give")
self.s_qr_give = QtWidgets.QToolButton(self.c_qr_code)
self.s_qr_give.setGeometry(QtCore.QRect(410, 210, 41, 27))
self.s_qr_give.setFont(font1)
self.s_qr_give.setObjectName("s_qr_give")
self.l_qr_dir = QtWidgets.QLabel(self.c_qr_code)
self.l_qr_dir.setGeometry(QtCore.QRect(30, 40, 281, 25))
self.l_qr_dir.setFont(font)
self.l_qr_dir.setObjectName("l_qr_dir")
self.i_qr_dir = QtWidgets.QLineEdit(self.c_qr_code)
self.i_qr_dir.setGeometry(QtCore.QRect(50, 71, 365, 25))
self.i_qr_dir.setFont(font1)
self.i_qr_dir.setObjectName("i_qr_dir")
self.s_qr_dir = QtWidgets.QToolButton(self.c_qr_code)
self.s_qr_dir.setGeometry(QtCore.QRect(410, 70, 41, 27))
self.s_qr_dir.setFont(font1)
self.s_qr_dir.setObjectName("s_qr_dir")
self.l_qr_user = QtWidgets.QLabel(self.c_qr_code)
self.l_qr_user.setGeometry(QtCore.QRect(30, 250, 251, 25))
self.l_qr_user.setFont(font)
self.l_qr_user.setObjectName("l_qr_user")
self.i_qr_user = QtWidgets.QLineEdit(self.c_qr_code)
self.i_qr_user.setGeometry(QtCore.QRect(50, 281, 365, 25))
self.i_qr_user.setFont(font1)
self.i_qr_user.setObjectName("i_qr_user")
self.s_qr_user = QtWidgets.QToolButton(self.c_qr_code)
self.s_qr_user.setGeometry(QtCore.QRect(410, 280, 41, 27))
self.s_qr_user.setFont(font1)
self.s_qr_user.setObjectName("s_qr_user")
self.l_qr_snps = QtWidgets.QLabel(self.c_qr_code)
self.l_qr_snps.setGeometry(QtCore.QRect(30, 110, 281, 25))
self.l_qr_snps.setFont(font)
self.l_qr_snps.setObjectName("l_qr_snps")
self.i_qr_snps = QtWidgets.QLineEdit(self.c_qr_code)
self.i_qr_snps.setGeometry(QtCore.QRect(50, 141, 365, 25))
self.i_qr_snps.setFont(font1)
self.i_qr_snps.setObjectName("i_qr_snps")
self.s_qr_snps = QtWidgets.QToolButton(self.c_qr_code)
self.s_qr_snps.setGeometry(QtCore.QRect(410, 140, 41, 27))
self.s_qr_snps.setFont(font1)
self.s_qr_snps.setObjectName("s_qr_snps")
self.b_default_qr_code = QtWidgets.QPushButton(self.QR_code)
self.b_default_qr_code.setGeometry(QtCore.QRect(230, 380, 91, 31))
self.b_default_qr_code.setFont(font)
self.b_default_qr_code.setObjectName("b_default_qr_code")
self.Function.addTab(self.QR_code, "")
# self.API = QtWidgets.QWidget()
# self.API.setObjectName("API")
# self.UMAP = QtWidgets.QGroupBox(self.API)
# self.UMAP.setEnabled(True)
# self.UMAP.setGeometry(QtCore.QRect(30, 10, 501, 161))
#
# self.UMAP.setFont(font)
# self.UMAP.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
# self.UMAP.setObjectName("UMAP")
# self.l_umap_ref = QtWidgets.QLabel(self.UMAP)
# self.l_umap_ref.setGeometry(QtCore.QRect(30, 31, 131, 25))
#
# self.l_umap_ref.setFont(font2)
# self.l_umap_ref.setObjectName("l_umap_ref")
# self.i_umap_ref = QtWidgets.QLineEdit(self.UMAP)
# self.i_umap_ref.setGeometry(QtCore.QRect(164, 32, 248, 25))
#
# self.i_umap_ref.setFont(font1)
# self.i_umap_ref.setObjectName("i_umap_ref")
# self.s_umap_ref = QtWidgets.QToolButton(self.UMAP)
# self.s_umap_ref.setGeometry(QtCore.QRect(410, 31, 41, 27))
#
# self.s_umap_ref.setFont(font1)
# self.s_umap_ref.setObjectName("s_umap_ref")
# self.l_umap_sample = QtWidgets.QLabel(self.UMAP)
# self.l_umap_sample.setGeometry(QtCore.QRect(30, 61, 131, 25))
#
# self.l_umap_sample.setFont(font2)
# self.l_umap_sample.setObjectName("l_umap_sample")
# self.i_umap_sample = QtWidgets.QLineEdit(self.UMAP)
# self.i_umap_sample.setGeometry(QtCore.QRect(164, 62, 248, 25))
#
# self.i_umap_sample.setFont(font1)
# self.i_umap_sample.setObjectName("i_umap_sample")
# self.s_umap_sample = QtWidgets.QToolButton(self.UMAP)
# self.s_umap_sample.setGeometry(QtCore.QRect(410, 61, 41, 27))
#
# self.s_umap_sample.setFont(font1)
# self.s_umap_sample.setObjectName("s_umap_sample")
# self.l_umap_metadata = QtWidgets.QLabel(self.UMAP)
# self.l_umap_metadata.setGeometry(QtCore.QRect(30, 90, 131, 25))
#
# self.l_umap_metadata.setFont(font2)
# self.l_umap_metadata.setObjectName("l_umap_metadata")
# self.s_umap_metadata = QtWidgets.QToolButton(self.UMAP)
# self.s_umap_metadata.setGeometry(QtCore.QRect(410, 90, 41, 27))
#
# self.s_umap_metadata.setFont(font1)
# self.s_umap_metadata.setObjectName("s_umap_metadata")
# self.i_umap_metadata = QtWidgets.QLineEdit(self.UMAP)
# self.i_umap_metadata.setGeometry(QtCore.QRect(164, 91, 248, 25))
#
# self.i_umap_metadata.setFont(font1)
# self.i_umap_metadata.setObjectName("i_umap_metadata")
# self.b_run_umap = QtWidgets.QPushButton(self.UMAP)
# self.b_run_umap.setGeometry(QtCore.QRect(170, 120, 181, 31))
#
# self.b_run_umap.setFont(font)
# self.b_run_umap.setObjectName("b_run_umap")
# self.add_rsid = QtWidgets.QGroupBox(self.API)
# self.add_rsid.setEnabled(True)
# self.add_rsid.setGeometry(QtCore.QRect(30, 180, 501, 111))
#
# self.add_rsid.setFont(font)
# self.add_rsid.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
# self.add_rsid.setObjectName("add_rsid")
# self.l_add_rsid_file = QtWidgets.QLabel(self.add_rsid)
# self.l_add_rsid_file.setGeometry(QtCore.QRect(30, 31, 131, 25))
#
# self.l_add_rsid_file.setFont(font2)
# self.l_add_rsid_file.setObjectName("l_add_rsid_file")
# self.i_add_rsid_file = QtWidgets.QLineEdit(self.add_rsid)
# self.i_add_rsid_file.setGeometry(QtCore.QRect(121, 32, 221, 25))
#
# self.i_add_rsid_file.setFont(font1)
# self.i_add_rsid_file.setObjectName("i_add_rsid_file")
# self.s_add_rsid_file = QtWidgets.QToolButton(self.add_rsid)
# self.s_add_rsid_file.setGeometry(QtCore.QRect(340, 31, 41, 27))
#
# self.s_add_rsid_file.setFont(font1)
# self.s_add_rsid_file.setObjectName("s_add_rsid_file")
# self.l_add_rsid_db = QtWidgets.QLabel(self.add_rsid)
# self.l_add_rsid_db.setGeometry(QtCore.QRect(30, 70, 131, 25))
#
# self.l_add_rsid_db.setFont(font2)
# self.l_add_rsid_db.setObjectName("l_add_rsid_db")
# self.i_add_rsid_db = QtWidgets.QLineEdit(self.add_rsid)
# self.i_add_rsid_db.setGeometry(QtCore.QRect(121, 71, 221, 25))
# self.s_add_rsid_db = QtWidgets.QToolButton(self.add_rsid)
# self.s_add_rsid_db.setGeometry(QtCore.QRect(340, 70, 41, 27))
#
# self.s_add_rsid_db.setFont(font1)
# self.s_add_rsid_db.setObjectName("s_add_rsid_db")
#
# self.i_add_rsid_db.setFont(font1)
# self.i_add_rsid_db.setObjectName("i_add_rsid_db")
# self.b_run_add_rsid = QtWidgets.QPushButton(self.add_rsid)
# self.b_run_add_rsid.setGeometry(QtCore.QRect(390, 33, 101, 61))
#
# self.b_run_add_rsid.setFont(font)
# self.b_run_add_rsid.setObjectName("b_run_add_rsid")
# self.qr_code = QtWidgets.QGroupBox(self.API)
# self.qr_code.setEnabled(True)
# self.qr_code.setGeometry(QtCore.QRect(30, 300, 501, 111))
#
# self.qr_code.setFont(font)
# self.qr_code.setContextMenuPolicy(QtCore.Qt.DefaultContextMenu)
# self.qr_code.setObjectName("qr_code")
# self.l_qr_code_snp = QtWidgets.QLabel(self.qr_code)
# self.l_qr_code_snp.setGeometry(QtCore.QRect(30, 31, 121, 25))
#
# self.l_qr_code_snp.setFont(font2)
# self.l_qr_code_snp.setObjectName("l_qr_code_snp")
# self.i_qr_code_snp = QtWidgets.QLineEdit(self.qr_code)
# self.i_qr_code_snp.setGeometry(QtCore.QRect(121, 32, 221, 25))
#
# self.i_qr_code_snp.setFont(font1)
# self.i_qr_code_snp.setObjectName("i_qr_code_snp")
# self.s_qr_code_snp = QtWidgets.QToolButton(self.qr_code)
# self.s_qr_code_snp.setGeometry(QtCore.QRect(340, 31, 41, 27))
#
# self.s_qr_code_snp.setFont(font1)
# self.s_qr_code_snp.setObjectName("s_qr_code_snp")
# self.b_run_qr_code = QtWidgets.QPushButton(self.qr_code)
# self.b_run_qr_code.setGeometry(QtCore.QRect(390, 33, 101, 61))
#
# self.b_run_qr_code.setFont(font)
# self.b_run_qr_code.setObjectName("b_run_qr_code")
# self.s_qr_code_key = QtWidgets.QToolButton(self.qr_code)
# self.s_qr_code_key.setGeometry(QtCore.QRect(340, 70, 41, 27))
#
# self.s_qr_code_key.setFont(font1)
# self.s_qr_code_key.setObjectName("s_qr_code_key")
# self.l_qr_code_key = QtWidgets.QLabel(self.qr_code)
# self.l_qr_code_key.setGeometry(QtCore.QRect(30, 70, 121, 25))
#
# self.l_qr_code_key.setFont(font2)
# self.l_qr_code_key.setObjectName("l_qr_code_key")
# self.i_qr_code_key = QtWidgets.QLineEdit(self.qr_code)
# self.i_qr_code_key.setGeometry(QtCore.QRect(121, 71, 221, 25))
#
# self.i_qr_code_key.setFont(font1)
# self.i_qr_code_key.setObjectName("i_qr_code_key")
# self.Function.addTab(self.API, "")
PAGEANT.setCentralWidget(self.MainWindow)
self.retranslateUi(PAGEANT)
self.Function.setCurrentIndex(0)
self.s_pop_sep.setCurrentIndex(0)
self.s_qual_pop.setCurrentIndex(-1)
self.s_quan_pop.setCurrentIndex(-1)
QtCore.QMetaObject.connectSlotsByName(PAGEANT)
self.l_database_quan.raise_()
self.i_database_quan.raise_()
self.i_ref_quan.raise_()
self.s_database_quan.raise_()
self.l_ref_quan.raise_()
self.l_quan_pop.raise_()
self.s_ref_quan.raise_()
self.s_quan_pop.raise_()
self.l_database_qual.raise_()
self.i_database_qual.raise_()
self.i_ref_qual.raise_()
self.s_database_qual.raise_()
self.l_ref_qual.raise_()
self.s_ref_qual.raise_()
self.g_qual.raise_()
self.b_default_qual.raise_()
self.i_output.raise_()
self.i_vcf.raise_()
self.b_analyze.raise_()
self.l_vcf.raise_()
self.l_output.raise_()
self.s_output.raise_()
self.l_name.raise_()
self.i_name.raise_()
self.s_vcf.raise_()
self.l_config.raise_()
self.i_config.raise_()
self.s_config.raise_()
self.l_ps_ref.raise_()
self.i_ps_ref.raise_()
self.s_ps_ref.raise_()
self.l_ps_pop.raise_()
self.i_pop.raise_()
self.l_pop.raise_()
self.l_pop_sep.raise_()
self.i_ps_pop.raise_()
self.i_pop_id.raise_()
self.l_pop_id.raise_()
self.s_pop_sep.raise_()
self.s_ps_pop.raise_()
def retranslateUi(self, PAGEANT):
_translate = QtCore.QCoreApplication.translate
PAGEANT.setWindowTitle(_translate("PAGEANT", f"PAGEANT ({main.version})"))
self.i_vcf.setToolTip(_translate("PAGEANT", "Select the genotype file that you want to analyze"))
self.i_vcf.setText(_translate("PAGEANT", "./personal_genome/HG001.vcf.gz"))
self.i_vcf.setPlaceholderText(_translate("PAGEANT", "Select the genotype file"))
self.b_analyze.setToolTip(_translate("PAGEANT", "Start analyze"))
self.b_analyze.setText(_translate("PAGEANT", "Analyze"))
self.s_vcf.setText(_translate("PAGEANT", "..."))
self.l_vcf.setToolTip(_translate("PAGEANT", "Input the genotype file that you want to analyze"))
self.l_vcf.setText(_translate("PAGEANT", "Genotype file"))
self.l_output.setText(_translate("PAGEANT", "Ouput Directory"))
self.i_output.setToolTip(_translate("PAGEANT", "Specify the output directory"))
self.i_output.setText(_translate("PAGEANT", os.path.join(os.getcwd(), 'output')))
self.i_output.setPlaceholderText(_translate("PAGEANT", 'Specify the output directory'))
self.s_output.setText(_translate("PAGEANT", "..."))
self.l_name.setText(_translate("PAGEANT", "Name"))
self.i_name.setToolTip(_translate("PAGEANT", "Input your name here"))
self.i_name.setText(_translate("PAGEANT", "HG001"))
self.l_config.setText(_translate("PAGEANT", "Configuration file"))
self.i_config.setToolTip(_translate("PAGEANT", "Specify the configuration file"))
self.i_config.setText(_translate("PAGEANT", "./bin/config.ini"))
self.i_config.setPlaceholderText(_translate("PAGEANT", "Specify the configuration file"))
self.s_config.setText(_translate("PAGEANT", "..."))
self.Function.setTabText(self.Function.indexOf(self.Basic), _translate("PAGEANT", "I/O"))
self.b_default_qual.setToolTip(_translate("PAGEANT", "Set default values"))
self.b_default_qual.setText(_translate("PAGEANT", "Default"))
self.g_qual.setTitle(_translate("PAGEANT", "Qualitative traits"))
self.l_database_qual.setText(_translate("PAGEANT", "Database directory"))
self.s_ref_qual.setText(_translate("PAGEANT", "..."))
self.i_database_qual.setToolTip(_translate("PAGEANT", "Specify directory of database for qualitative traits"))
self.i_database_qual.setText(_translate("PAGEANT", "./algorithm/Qualitative"))
self.i_database_qual.setPlaceholderText(_translate("PAGEANT", "Specify database for qualitative traits"))
self.i_ref_qual.setToolTip(_translate("PAGEANT", "Specify directory of reference for qualitative traits"))
self.i_ref_qual.setText(_translate("PAGEANT", "./population_genome/g1k_ref"))
self.i_ref_qual.setPlaceholderText(_translate("PAGEANT", "Specify reference for qualitative traits"))
self.s_database_qual.setText(_translate("PAGEANT", "..."))
self.l_ref_qual.setText(_translate("PAGEANT", "Reference population directory"))
self.l_qual_pop.setText(_translate("PAGEANT", "Reference population ethnic group"))
self.Function.setTabText(self.Function.indexOf(self.Qualitative), _translate("PAGEANT", "Qualitative"))
self.b_default_quan.setToolTip(_translate("PAGEANT", "Set default values"))
self.b_default_quan.setText(_translate("PAGEANT", "Default"))
self.g_quan.setTitle(_translate("PAGEANT", "Quantitative traits"))
self.l_database_quan.setText(_translate("PAGEANT", "Database directory"))
self.s_ref_quan.setText(_translate("PAGEANT", "..."))
self.i_database_quan.setToolTip(_translate("PAGEANT", "Specify directory of database for quantitative traits"))
self.i_database_quan.setText(_translate("PAGEANT", "./algorithm/Quantitative"))
self.i_database_quan.setPlaceholderText(_translate("PAGEANT", "Specify database for quantitative traits"))
self.i_ref_quan.setToolTip(_translate("PAGEANT", "Specify directory of reference for quantitative traits"))
self.i_ref_quan.setText(_translate("PAGEANT", "./population_genome/g1k_ref"))
self.i_ref_quan.setPlaceholderText(_translate("PAGEANT", "Specify reference for quantitative traits"))
self.s_database_quan.setText(_translate("PAGEANT", "..."))
self.l_ref_quan.setText(_translate("PAGEANT", "Reference population directory"))
self.l_quan_pop.setText(_translate("PAGEANT", "Reference population ethnic group"))
self.PRS.setTitle(_translate("PAGEANT", "PRS methods"))
self.l_p1.setToolTip(_translate("PAGEANT", "Index variant p-value threshold"))
self.l_p1.setText(_translate("PAGEANT", "p1"))
self.i_p1.setToolTip(_translate("PAGEANT", "Index variant p-value threshold"))
self.i_p1.setText(_translate("PAGEANT", "5e-8"))
self.l_r2.setToolTip(_translate("PAGEANT", "r^2 threshold"))
self.l_r2.setText(_translate("PAGEANT", "r2"))
self.i_r2.setToolTip(_translate("PAGEANT", "<html><head/><body><p>r<span style=\" vertical-align:super;\">"
"2</span> threshold</p></body></html>"))
self.i_r2.setText(_translate("PAGEANT", "0.1"))
self.l_kb.setToolTip(_translate("PAGEANT", "Clump kb radius"))
self.l_kb.setText(_translate("PAGEANT", "kb"))
self.i_kb.setToolTip(_translate("PAGEANT", "Clump kb radius"))