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)