def __init__(self, folder, directory, gene_list_file, *args):
super(Read_Depth_Gui, self).__init__(*args)
self.setupUi(self)
self.input_folder = folder
self.interval = 100
self.interval_spin.setValue(100)
self.allowed_mismatches = 1
self.directory = directory
self.gene_list_file = gene_list_file
self.fileio = f.fileio()
self.list_of_reads = []
self.plot = plot.RDPlot("Base Pair", "# Hits")
self.selected_accession_number_name = ''
self.selected_gene = {}
self.dataset_name = '-- Select --'
self.gene_list = OrderedDict()
self.datasets_cache = OrderedDict()
self.accession_numbers_list = QtCore.QStringList()
self._initialize_ui_elements()
self.process = process.process()
self.read_list_thread = GetReadList_Thread(self.directory, self.input_folder, self.dataset_name,
self.selected_gene, self)
self.connect(self.read_list_thread, QtCore.SIGNAL("GeneListFinished"), self.dataset_loaded)
self.calculate_depth_thread = CalculateDepth_Thread(self)
self.connect(self.calculate_depth_thread, QtCore.SIGNAL("CalculateDepthFinished"), self.load_table_w_data)
def __init__(self, folder, directory, gene_list_file, *args):
super(Read_Depth_Gui, self).__init__(*args)
self.setupUi(self)
self.input_folder = folder
self.interval = 100
self.interval_spin.setValue(100)
self.allowed_mismatches = 1
self.directory = directory
self.gene_list_file = gene_list_file
self.fileio = f.fileio()
self.list_of_reads = []
self.plot = plot.RDPlot("Base Pair", "# Hits")
self.selected_accession_number_name = ''
self.selected_gene = {}
self.dataset_name = '-- Select --'
self.gene_list = OrderedDict()
self.datasets_cache = OrderedDict()
self.accession_numbers_list = QtCore.QStringList()
self._initialize_ui_elements()
self.process = process.process()
self.read_list_thread = GetReadList_Thread(self.directory,
self.input_folder,
self.dataset_name,
self.selected_gene, self)
self.connect(self.read_list_thread, QtCore.SIGNAL("GeneListFinished"),
self.dataset_loaded)
self.calculate_depth_thread = CalculateDepth_Thread(self)
self.connect(self.calculate_depth_thread,
QtCore.SIGNAL("CalculateDepthFinished"),
self.load_table_w_data)
def __init__(self, folder, directory, list_file, *args):
super(Query_Blast_Gui, self).__init__(*args)
self.setupUi(self)
self.clipboard = ""
self.input_folder = folder
self.directory = directory
self.list_file = list_file
self.updating = False
self.fileio = f.fileio()
# Selections from GUI
self.selected_gene_name = ''
self.selected_accession_number = ''
self.selected_dataset_names = [
'-- Select --', '-- Select --', '-- Select --'
]
# Generic Table Names
self.table = None
self.table_filtered = None
# Cache for storing data
self.gene_info_list = OrderedDict()
self.accession_number_list = OrderedDict()
self.datasets_cache = OrderedDict()
self.sequences_info_list = {}
# Methods
self._initialize_ui_elements()
# Results Store
self.results = [[], [], []]
self.filtered_results = [[], [], []]
self.graph1 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_1.addTab(self.graph1, "Plot")
self.graph1.initialize_plot()
self.graph2 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_2.addTab(self.graph2, "Plot")
self.graph2.initialize_plot()
self.graph3 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_3.addTab(self.graph3, "Plot")
self.graph3.initialize_plot()
def __init__(self, folder, directory, gene_list_file, *args):
super(Query_Blast_Gui, self).__init__(*args)
self.setupUi(self)
self.input_folder = folder
self.directory = directory
self.gene_list_file = gene_list_file
self.fileio = f.fileio()
# Selections from GUI
self.selected_accession_number_name = ''
self.selected_dataset_names = ['-- Select --', '-- Select --', '-- Select --']
# Generic Table Names
self.table = None
self.table_filtered = None
# Cache for storing data
self.selected_gene = {}
self.gene_information = OrderedDict()
self.datasets_cache = OrderedDict()
self.accession_numbers_list = QtCore.QStringList()
# Methods
self._initialize_ui_elements()
# Results Store
self.results = [[], [], []]
self.filtered_results = [[], [], []]
self.graph1 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_1.addTab(self.graph1, "Plot")
self.graph1.initialize_plot()
self.graph2 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_2.addTab(self.graph2, "Plot")
self.graph2.initialize_plot()
self.graph3 = plot.QBPlot('Base Pair', 'Junction Count (ppm)')
self.tabWidget_3.addTab(self.graph3, "Plot")
self.graph3.initialize_plot()
print ">>> Using %d Processor Cores" % (num_cores - 1)
_spin = spinbar.SpinCursor(msg="Processing mapped .sam files ...", speed=2)
_spin.start()
Parallel.Parallel(n_jobs=num_cores-1)(Parallel.delayed(letsCount)(directory, summary_folder, chromosomes_folder,
input_folder, chromosomes_list, f) for f in
sam_file_list)
_spin.stop()
def initialize_folders(directory):
# Creates the folder that will hold the Genecounts summaries
fileio.create_new_folder(directory, summary_folder)
# Creates the folder that will hold more granualar data on exon counts per chromosome
fileio.create_new_folder(directory, chromosomes_folder)
fileio.create_new_folder(directory, "gene_count_indices")
if __name__ == '__main__':
# Instantiate Function Objects for Basic Input Output
printio = p.printio()
fileio = f.fileio()
sys.stdout.write("\n*** Running Gene Count Y2H ***\n\n")
sys.stdout.flush()
initialize_folders(main_directory)
# Makes sure proper files are in their place and returns .sam file list
sam_file_list = fileio.get_sam_filelist(main_directory, input_folder)
# Gets list of chromosomes from Y2Hreadme.txt file
chromosomes_list = fileio.get_chromosomes_list(main_directory, chromosomes_list_name, printio)
gene_count(main_directory, summary_folder, chromosomes_folder, input_folder, chromosomes_list, sam_file_list)
import os
def __init__(self, *args):
super(DEEPN_Launcher, self).__init__(*args)
self.setupUi(self)
self.proceed = 1
self.prompt = 2
self.fileio = f.fileio()
self.printio = p.printio()
self.directory = None
self.clicked_button = None
self.clicked_button_text = None
self.db_selection = None
self.combined = 0
self.blast_db_name = ''
self.gene_dictionary = ''
self.gene_list_file = ''
self.chromosome_list = ''
self.start_match = re.compile(r'^[>>>|\t|***]')
self.bar = itertools.cycle(['/', '-', '\\'])
self._layouts = [
self.analyze_data_layout, self.process_data_layout_1,
self.process_data_layout_2, self.process_data_layout_3,
self.process_data_layout_4, self.status_layout
]
self.window = self.window()
self.window.setGeometry(10, 30, self.width(), self.height())
self.buttons = []
self.thread = None
self.message = m.Message_Dialog()
self.comment = m.Message_Dialog()
self.quit = False
for layout in self._layouts:
widgets = (layout.itemAt(i).widget()
for i in range(layout.count()))
for btn in widgets:
if btn != None:
self.buttons.append(btn)
self.buttons1 = []
widgets = (self.layout1.itemAt(i).widget()
for i in range(self.layout1.count()))
for btn in widgets:
if btn != None:
self.buttons1.append(btn)
# Checkbox
self.prompt_box.stateChanged.connect(self.on_prompt_box_stateChanged)
# QProcess object for external app
self.process = QtCore.QProcess(self)
self.process.readyReadStandardOutput.connect(self.stdout_ready)
# self.process.readyReadStandardError.connect(self.stderr_ready)
self.process.started.connect(self.process_started)
self.process.finished.connect(self.process_finished)
# QThread for processes
self.thread = QtCore.QThread(self)
# Connect database
self.g_db = db.genome_db(os.path.join('DEEPN_db.sqlite3'))
for row in self.g_db.select_all('*'):
self.db_list_wgt.addItem(vQlistWidgetItem(row[1], row[0]))
# Binding Selection Changed Signal
self.db_list_wgt.itemSelectionChanged.connect(self.selection_changed)
# Disable All buttons
self.disable_unused_buttons()
for btn in self.buttons1:
btn.setEnabled(False)
self.message.quit_btn.clicked.connect(self.message_quit_signal)
self.message.continue_btn.clicked.connect(self.message_continue_signal)
self.comment.continue_btn.clicked.connect(self.comment_continue_signal)
self.comment.quit_btn.setEnabled(False)
lets_count)(directory, summary_folder, chromosomes_folder,
input_folder, chromosomes_list, f) for f in sam_file_list)
def initialize_folders(directory):
# Creates the folder that will hold the Genecounts summaries
fileio.create_new_folder(directory, summary_folder)
# Creates the folder that will hold more granualar data on exon counts per chromosome
fileio.create_new_folder(directory, chromosomes_folder)
fileio.create_new_folder(directory, "gene_count_indices")
if __name__ == '__main__':
# Instantiate Function Objects for Basic Input Output
printio = p.printio()
fileio = f.fileio()
sys.stdout.write("\n*** Running Gene Count Y2H ***\n\n")
sys.stdout.flush()
initialize_folders(main_directory)
# Makes sure proper files are in their place and returns .sam file list
sam_file_list = fileio.get_sam_filelist(main_directory, input_folder)
processed_file_list = fileio.get_file_list(main_directory, summary_folder,
".csv")
for processed_file in processed_file_list:
for sam_file in sam_file_list:
if processed_file.replace("_summary.csv", "") == sam_file[:-4]:
sam_file_list.remove(sam_file)
break
# Gets list of chromosomes from Y2Hreadme.txt file
def __init__(self, *args):
super(DEEPN_Launcher, self).__init__(*args)
self.setupUi(self)
self.proceed = 1
self.prompt = 2
self.fileio = f.fileio()
self.printio = p.printio()
self.directory = None
self.clicked_button = None
self.clicked_button_text = None
self.db_selection = None
self.blast_db_name = ''
self.gene_dictionary = ''
self.gene_list_file = ''
self.chromosome_list = ''
self.start_match = re.compile(r'^[>>>|\t|***]')
self.bar = itertools.cycle(['/', '-', '\\'])
self._layouts = [self.analyze_data_layout, self.process_data_layout_1,
self.process_data_layout_2, self.process_data_layout_3,
self.process_data_layout_4, self.status_layout]
self.window = self.window()
self.window.setGeometry(10, 30, self.width(), self.height())
self.buttons = []
self.thread = None
self.message = m.Message_Dialog()
self.comment = m.Message_Dialog()
self.quit = False
for layout in self._layouts:
widgets = (layout.itemAt(i).widget() for i in range(layout.count()))
for btn in widgets:
if btn != None:
self.buttons.append(btn)
self.buttons1 = []
widgets = (self.layout1.itemAt(i).widget() for i in range(self.layout1.count()))
for btn in widgets:
if btn != None:
self.buttons1.append(btn)
# Checkbox
self.prompt_box.stateChanged.connect(self.on_prompt_box_stateChanged)
# QProcess object for external app
self.process = QtCore.QProcess(self)
self.process.readyReadStandardOutput.connect(self.stdout_ready)
# self.process.readyReadStandardError.connect(self.stderr_ready)
self.process.started.connect(self.process_started)
self.process.finished.connect(self.process_finished)
# QThread for processes
self.thread = QtCore.QThread(self)
# Connect database
self.g_db = db.genome_db(os.path.join('DEEPN_db.sqlite3'))
for row in self.g_db.select_all('*'):
self.db_list_wgt.addItem(vQlistWidgetItem(row[1], row[0]))
# Binding Selection Changed Signal
self.db_list_wgt.itemSelectionChanged.connect(self.selection_changed)
# Disable All buttons
self.disable_unused_buttons()
for btn in self.buttons1:
btn.setEnabled(False)
self.message.quit_btn.clicked.connect(self.message_quit_signal)
self.message.continue_btn.clicked.connect(self.message_continue_signal)
self.comment.continue_btn.clicked.connect(self.comment_continue_signal)
self.comment.quit_btn.setEnabled(False)
