from pathlib import Path from threading import Thread from time import sleep from tkinter import filedialog import customtkinter from rich import print from metaDMG.cli import cli_utils #%% # Modes: "System" (standard), "Dark", "Light" customtkinter.set_appearance_mode("dark") # Themes: "blue" (standard), "green", "dark-blue" customtkinter.set_default_color_theme("blue") FONT = customtkinter.ThemeManager.theme["text"]["font"] #%% def format_directory(path: Path): return path.name + "/" def path_to_text(filepath: str, cut: int = 10) -> str: text = Path(filepath).name if len(text) > cut: text = text[:cut] + " ..." return text #%% KW_OPTIONS_MENU = dict( fg_color="gray30", button_color="gray50", button_hover_color="gray60", ) KW_OPTIONS_MENU_DISABLED = dict( fg_color="gray25", button_color="gray30", ) KW_BUTTON_BASE = dict( hover=True, border_width=2, text_color_disabled="gray40", ) KW_BUTTON_GOOD_COLORS = dict( fg_color=None, hover_color="gray30", border_color="gray30", ) KW_BUTTON_BAD_COLORS = dict( hover_color="#78413d", border_color="#78413d", fg_color="#603431", ) KW_ENTRY_GOOD_COLORS = dict( border_color="gray30", text_color="gray90", placeholder_text_color="gray90", fg_color="#2A2D2E", ) KW_ENTRY_DISABLED = dict( border_color="gray30", text_color="gray40", placeholder_text_color="gray40", fg_color="#2A2D2E", ) KW_ENTRY_BAD_COLORS = dict( border_color="#78413d", text_color="gray90", placeholder_text_color="gray90", fg_color="#603431", ) KW_SWITCH = dict(button_color="gray80") KW_SWITCH_DISABLED = dict(button_color="gray40") KW_SLIDER = dict( button_color="#1F6AA5", progress_color="#AAB0B5", ) KW_SLIDER_DISABLED = dict( button_color="gray40", progress_color="gray40", ) TOP_LABEL_WIDTH = 50 TOP_LABEL_PAD_X = 20 TOP_LABEL_GRID_KW = dict( pady=12, padx=TOP_LABEL_PAD_X, sticky="nsw", ) CENTER_LABEL_WIDTH = 50 CENTER_LABEL_PAD_X = 20 CENTER_LABEL_GRID_KW = dict( pady=12, padx=CENTER_LABEL_PAD_X, sticky="nsw", ) RIGHT_LABEL_WIDTH = 50 RIGHT_LABEL_PAD_X = 20 RIGHT_LABEL_GRID_KW = dict( pady=12, padx=RIGHT_LABEL_PAD_X, sticky="nsw", ) #%% class Gui(customtkinter.CTk): def __init__(self, verbose: bool = True): super().__init__() self.verbose = verbose self.title("MetaDMG Configuirator") WIDTH = 785 HEIGHT = 655 X, Y = self.get_center_coordinates(WIDTH, HEIGHT) self.geometry(f"{WIDTH}x{HEIGHT}+{X}+{Y}") self.resizable(False, False) # call .on_closing() when app gets closed self.protocol("WM_DELETE_WINDOW", self.on_closing) # ============ create frames ============ self.setup_header() # ============ frame_top ============ self.setup_top_frame() # ============ frame_center ============ self.setup_center_frame() # ============ frame_right ============ self.setup_right_frame() # ============ background threads ============ self.start_similarity_scores_background_thread() self.start_minimum_reads_background_thread() # ============ HEADER ============ def setup_header(self): self.headline = customtkinter.CTkLabel( master=self, justify="center", text="Confi-gui-rator", text_font=(FONT, "-30"), ) self.headline.grid( row=0, column=0, columnspan=2, ) # ============ TOP FRAME ============ def setup_top_frame(self): self.frame_top = customtkinter.CTkFrame( master=self, ) self.frame_top.grid( row=1, column=0, sticky="nswe", padx=20, pady=20, ) # # empty row with minsize as spacing # self.frame_top.grid_rowconfigure(0, minsize=50) # # empty row with minsize as spacing self.frame_top.grid_columnconfigure(1, minsize=80) self.TOP_LABEL_KW = dict(master=self.frame_top, width=TOP_LABEL_WIDTH) self.setup_bam_file() self.setup_damage_mode() # ============ BAM FILE ============ def setup_bam_file(self): self.bam_label = customtkinter.CTkLabel( text="BAM file:", **self.TOP_LABEL_KW, ) self.bam_label.grid( row=0, column=0, **TOP_LABEL_GRID_KW, ) self.bam_file_path = None self.bam_button = customtkinter.CTkButton( master=self.frame_top, text="Select file", command=self.bam_callback, **KW_BUTTON_BASE, **KW_BUTTON_BAD_COLORS, ) self.bam_button.grid( row=0, column=2, pady=12, sticky="e", ) self.bam_is_okay = False # ============ DAMAGE MODE ============ def setup_damage_mode(self): self.damage_mode_label = customtkinter.CTkLabel( text="Damage Mode:", **self.TOP_LABEL_KW, ) self.damage_mode_label.grid( row=1, column=0, **TOP_LABEL_GRID_KW, ) self.damage_mode_value = cli_utils.DAMAGE_MODE.LCA self.damage_mode_menu = customtkinter.CTkOptionMenu( master=self.frame_top, values=cli_utils.DAMAGE_MODE.list(), command=self.damage_mode_collback, **KW_OPTIONS_MENU, ) self.damage_mode_menu.grid( row=1, column=2, pady=12, sticky="e", ) self.is_lca = True # ============ CENTER FRAME ============ def setup_center_frame(self): self.frame_center = customtkinter.CTkFrame( master=self, ) self.frame_center.grid( row=2, column=0, sticky="nswe", padx=20, # pady=20, ) # configure grid layout (3 x 2) (row x column) self.frame_center.grid_rowconfigure(0, minsize=10) self.CENTER_LABEL_KW = dict(master=self.frame_center, width=CENTER_LABEL_WIDTH) self.setup_names() self.setup_nodes() self.setup_acc2tax() self.setup_similarity_score() self.setup_min_mapping_quality() self.setup_custom_database() self.setup_lca_rank() # ============ NAMES ============ def setup_names(self): # self.names_file_string = customtkinter.StringVar() self.names_file_path = None self.names_label = customtkinter.CTkLabel( text="Names:", **self.CENTER_LABEL_KW, ) self.names_label.grid( row=1, column=0, **CENTER_LABEL_GRID_KW, ) self.names_button = customtkinter.CTkButton( master=self.frame_center, text="Select file", command=self.names_callback, **KW_BUTTON_BASE, **KW_BUTTON_BAD_COLORS, ) self.names_button.grid( row=1, column=1, pady=12, padx=10, ) self.names_is_okay = False self.names_button_colors = KW_BUTTON_BAD_COLORS # ============ NODES ============ def setup_nodes(self): self.nodes_file_path = None self.nodes_label = customtkinter.CTkLabel( text="Nodes:", **self.CENTER_LABEL_KW, ) self.nodes_label.grid( row=2, column=0, **CENTER_LABEL_GRID_KW, ) self.nodes_button = customtkinter.CTkButton( master=self.frame_center, text="Select file", command=self.nodes_callback, **KW_BUTTON_BASE, **KW_BUTTON_BAD_COLORS, ) self.nodes_button.grid( row=2, column=1, pady=12, padx=10, ) self.nodes_is_okay = False self.nodes_button_colors = KW_BUTTON_BAD_COLORS # ============ ACC2TAX ============ def setup_acc2tax(self): self.acc2tax_file_path = None self.acc2tax_label = customtkinter.CTkLabel( text="Acc2tax:", **self.CENTER_LABEL_KW, ) self.acc2tax_label.grid( row=3, column=0, **CENTER_LABEL_GRID_KW, ) self.acc2tax_button = customtkinter.CTkButton( master=self.frame_center, text="Select file", command=self.acc2tax_callback, **KW_BUTTON_BASE, **KW_BUTTON_BAD_COLORS, ) self.acc2tax_button.grid( row=3, column=1, pady=12, padx=10, ) self.acc2tax_is_okay = False self.acc2tax_button_colors = KW_BUTTON_BAD_COLORS # ============ SIMILARITY SCORE ============ def setup_similarity_score(self): self.similarity_score_label = customtkinter.CTkLabel( text="Similarity Score:", **self.CENTER_LABEL_KW, ) self.similarity_score_label.grid( row=4, column=0, **CENTER_LABEL_GRID_KW, ) self.frame_similarity = customtkinter.CTkFrame( master=self.frame_center, fg_color="#2A2D2E", ) self.frame_similarity.grid( row=4, column=1, columnspan=3, rowspan=1, # pady=20, padx=30, sticky="w", ) self.similarity_score_min_value = customtkinter.StringVar( value="0.95", ) self.similarity_score_min = customtkinter.CTkEntry( master=self.frame_similarity, textvariable=self.similarity_score_min_value, width=40, **KW_ENTRY_GOOD_COLORS, ) self.similarity_score_min.grid( row=0, column=0, # sticky="nse", ) self.similarity_score_to = customtkinter.CTkLabel( master=self.frame_similarity, text="to", width=20, ) self.similarity_score_to.grid( row=0, column=1, # sticky="ns", ) self.similarity_score_max_value = customtkinter.StringVar( value="1.0", ) self.similarity_score_max = customtkinter.CTkEntry( master=self.frame_similarity, textvariable=self.similarity_score_max_value, width=40, **KW_ENTRY_GOOD_COLORS, ) self.similarity_score_max.grid( row=0, column=2, # sticky="nsw", ) # ============ MIN MAPPING QUALITY ============ def setup_min_mapping_quality(self): MIN_MAPPING_QUALITY_MIN = 0 MIN_MAPPING_QUALITY_DEFAULT = 0 MIN_MAPPING_QUALITY_MAX = 50 self.min_mapping_quality_label = customtkinter.CTkLabel( text="Minimum Mapping Quality:", **self.CENTER_LABEL_KW, ) self.min_mapping_quality_label.grid( row=5, column=0, **CENTER_LABEL_GRID_KW, ) self.frame_min_mapping_quality = customtkinter.CTkFrame( master=self.frame_center, fg_color="#2A2D2E", ) self.frame_min_mapping_quality.grid( row=5, column=1, sticky="e", ) self.min_mapping_quality_slider = customtkinter.CTkSlider( master=self.frame_min_mapping_quality, command=self.min_mapping_quality_slider_callback, from_=MIN_MAPPING_QUALITY_MIN, to=MIN_MAPPING_QUALITY_MAX, number_of_steps=MIN_MAPPING_QUALITY_MAX - MIN_MAPPING_QUALITY_MIN, width=100, **KW_SLIDER, ) self.min_mapping_quality_slider.set(MIN_MAPPING_QUALITY_DEFAULT) self.min_mapping_quality_slider.grid( row=0, column=0, sticky="e", ) self.min_mapping_quality_value = customtkinter.CTkLabel( master=self.frame_min_mapping_quality, width=20, ) self.min_mapping_quality_slider_callback(MIN_MAPPING_QUALITY_DEFAULT) self.min_mapping_quality_value.grid( row=0, column=1, pady=12, padx=0, ) # ============ CUSTOM DATABASE ============ def setup_custom_database(self): self.custom_database_label = customtkinter.CTkLabel( text="Custom Database:", **self.CENTER_LABEL_KW, ) self.custom_database_label.grid( row=6, column=0, **CENTER_LABEL_GRID_KW, ) self.custom_database_bool = customtkinter.BooleanVar() self.custom_database_button_title = customtkinter.StringVar( value="False", ) self.custom_database_switch = customtkinter.CTkSwitch( master=self.frame_center, textvariable=self.custom_database_button_title, command=self.custom_database_callback, onvalue=True, offvalue=False, **KW_SWITCH, ) self.custom_database_switch.deselect() self.custom_database_switch.grid( row=6, column=1, ) # ============ LCA RANK ============ def setup_lca_rank(self): self.lca_rank_label = customtkinter.CTkLabel( text="LCA Rank:", **self.CENTER_LABEL_KW, ) self.lca_rank_label.grid( row=7, column=0, **CENTER_LABEL_GRID_KW, ) self.lca_rank_string = customtkinter.StringVar( value=cli_utils.RANKS.none, ) self.lca_rank_menu = customtkinter.CTkOptionMenu( master=self.frame_center, values=cli_utils.RANKS.str_list(), command=self.lca_rank_callback, text_color_disabled="gray40", **KW_OPTIONS_MENU, ) self.lca_rank_menu.set("none") # set initial value self.lca_rank_menu.grid( row=7, column=1, ) # ============ RIGHT FRAME ============ def setup_right_frame(self): self.frame_right = customtkinter.CTkFrame( master=self, ) self.frame_right.grid( row=1, column=1, # sticky="e", # sticky="nswe", rowspan=3, # padx=20, pady=20, ) # configure grid layout (3 x 2) (row x column) self.frame_right.grid_rowconfigure(0, minsize=10) self.RIGHT_LABEL_KW = dict( master=self.frame_right, width=RIGHT_LABEL_WIDTH, ) self.setup_max_position() self.setup_min_reads() self.setup_bayesian() self.setup_forward() self.setup_parallel_samples() self.setup_cores_per_sample() self.setup_prefix() self.setup_suffix() self.setup_long_name() self.setup_config_name() self.setup_output_dir() self.setup_save_config() # ============ MAX POSITION ============ def setup_max_position(self): MAX_POSITION_MIN = 1 MAX_POSITION_DEFAULT = 15 MAX_POSITION_MAX = 30 self.max_position_label = customtkinter.CTkLabel( text="Maximum Position:", **self.RIGHT_LABEL_KW, ) self.max_position_label.grid( row=1, column=0, **RIGHT_LABEL_GRID_KW, ) self.frame_max_position = customtkinter.CTkFrame( master=self.frame_right, fg_color="#2A2D2E", ) self.frame_max_position.grid( row=1, column=1, sticky="e", ) self.max_position_slider = customtkinter.CTkSlider( master=self.frame_max_position, command=self.max_position_slider_callback, from_=MAX_POSITION_MIN, to=MAX_POSITION_MAX, number_of_steps=MAX_POSITION_MAX - MAX_POSITION_MIN, width=100, **KW_SLIDER, ) self.max_position_slider.set(MAX_POSITION_DEFAULT) self.max_position_slider.grid( row=0, column=0, sticky="e", ) self.max_position_value = customtkinter.CTkLabel( master=self.frame_max_position, width=20, ) self.max_position_value.grid( row=0, column=1, pady=12, padx=0, ) self.max_position_slider_callback(MAX_POSITION_DEFAULT) # ============ MINIMUM READS ============ def setup_min_reads(self): self.min_reads_label = customtkinter.CTkLabel( text="Minimum number of reads:", **self.RIGHT_LABEL_KW, ) self.min_reads_label.grid( row=2, column=0, **RIGHT_LABEL_GRID_KW, ) self.min_reads_value = customtkinter.StringVar( value="0", ) self.min_reads_entry = customtkinter.CTkEntry( master=self.frame_right, textvariable=self.min_reads_value, **KW_ENTRY_GOOD_COLORS, ) self.min_reads_entry.grid( row=2, column=1, ) # ============ BAYESIAN ============ def setup_bayesian(self): self.bayesian_label = customtkinter.CTkLabel( text="Bayesian:", **self.RIGHT_LABEL_KW, ) self.bayesian_label.grid( row=3, column=0, **RIGHT_LABEL_GRID_KW, ) self.bayesian_bool = customtkinter.BooleanVar() self.bayesian_button_title = customtkinter.StringVar( value="False", ) self.bayesian_switch = customtkinter.CTkSwitch( master=self.frame_right, textvariable=self.bayesian_button_title, command=self.bayesian_callback, onvalue=True, offvalue=False, **KW_SWITCH, ) self.bayesian_switch.deselect() self.bayesian_switch.grid( row=3, column=1, ) # ============ FORWARD ============ def setup_forward(self): self.forward_label = customtkinter.CTkLabel( text="Forward only:", **self.RIGHT_LABEL_KW, ) self.forward_label.grid( row=4, column=0, **RIGHT_LABEL_GRID_KW, ) self.forward_bool = customtkinter.BooleanVar() self.forward_button_title = customtkinter.StringVar( value="False", ) self.forward_switch = customtkinter.CTkSwitch( master=self.frame_right, textvariable=self.forward_button_title, command=self.forward_callback, onvalue=True, offvalue=False, **KW_SWITCH, ) self.forward_switch.deselect() self.forward_switch.grid( row=4, column=1, ) # ============ PARALLEL SAMPLES ============ def setup_parallel_samples(self): self.parallel_label = customtkinter.CTkLabel( text="Samples in parallel:", **self.RIGHT_LABEL_KW, ) self.parallel_label.grid( row=5, column=0, **RIGHT_LABEL_GRID_KW, ) self.frame_parallel_samples = customtkinter.CTkFrame( master=self.frame_right, fg_color="#2A2D2E", ) self.frame_parallel_samples.grid( row=5, column=1, sticky="e", ) PARALLEL_SAMPLES_MIN = 1 PARALLEL_SAMPLES_DEFAULT = 1 PARALLEL_SAMPLES_MAX = 20 self.parallel_samples_slider = customtkinter.CTkSlider( master=self.frame_parallel_samples, command=self.parallel_samples_slider_callback, from_=PARALLEL_SAMPLES_MIN, to=PARALLEL_SAMPLES_MAX, number_of_steps=PARALLEL_SAMPLES_MAX - PARALLEL_SAMPLES_MIN, width=100, **KW_SLIDER, ) self.parallel_samples_slider.set(PARALLEL_SAMPLES_DEFAULT) self.parallel_samples_slider.grid( row=0, column=0, sticky="e", ) self.parallel_samples_value = customtkinter.CTkLabel( master=self.frame_parallel_samples, width=20, ) self.parallel_samples_value.grid( row=0, column=1, pady=12, padx=0, ) self.parallel_samples_slider_callback(PARALLEL_SAMPLES_DEFAULT) # ============ CORES PR. SAMPLE ============ def setup_cores_per_sample(self): self.cores_per_sample_label = customtkinter.CTkLabel( text="Cores pr. sample:", **self.RIGHT_LABEL_KW, ) self.cores_per_sample_label.grid( row=6, column=0, **RIGHT_LABEL_GRID_KW, ) self.frame_cores_per_sample = customtkinter.CTkFrame( master=self.frame_right, fg_color="#2A2D2E", ) self.frame_cores_per_sample.grid( row=6, column=1, sticky="e", ) PARALLEL_CORES_PER_SAMPLE_MIN = 1 PARALLEL_CORES_PER_SAMPLE_DEFAULT = 1 PARALLEL_CORES_PER_SAMPLE_MAX = 20 self.cores_per_sample_slider = customtkinter.CTkSlider( master=self.frame_cores_per_sample, command=self.cores_per_sample_slider_callback, from_=PARALLEL_CORES_PER_SAMPLE_MIN, to=PARALLEL_CORES_PER_SAMPLE_MAX, number_of_steps=PARALLEL_CORES_PER_SAMPLE_MAX - PARALLEL_CORES_PER_SAMPLE_MIN, width=100, **KW_SLIDER, ) self.cores_per_sample_slider.set(PARALLEL_CORES_PER_SAMPLE_DEFAULT) self.cores_per_sample_slider.grid( row=0, column=0, sticky="e", ) self.cores_per_sample_value = customtkinter.CTkLabel( master=self.frame_cores_per_sample, width=20, ) self.cores_per_sample_value.grid( row=0, column=1, pady=12, padx=0, ) self.cores_per_sample_slider_callback(PARALLEL_CORES_PER_SAMPLE_DEFAULT) # ============ PREFIX ============ def setup_prefix(self): self.prefix_label = customtkinter.CTkLabel( text="Prefix:", **self.RIGHT_LABEL_KW, ) self.prefix_label.grid( row=7, column=0, **RIGHT_LABEL_GRID_KW, ) self.prefix_entry = customtkinter.CTkEntry( master=self.frame_right, placeholder_text="", **KW_ENTRY_GOOD_COLORS, ) self.prefix_entry.grid( row=7, column=1, ) # ============ SUFFIX ============ def setup_suffix(self): self.suffix_label = customtkinter.CTkLabel( text="Suffix:", **self.RIGHT_LABEL_KW, ) self.suffix_label.grid( row=8, column=0, **RIGHT_LABEL_GRID_KW, ) self.suffix_entry = customtkinter.CTkEntry( master=self.frame_right, placeholder_text="", **KW_ENTRY_GOOD_COLORS, ) self.suffix_entry.grid( row=8, column=1, ) # ============ LONG NAME ============ def setup_long_name(self): self.long_name_label = customtkinter.CTkLabel( text="Long name:", **self.RIGHT_LABEL_KW, ) self.long_name_label.grid( row=9, column=0, **RIGHT_LABEL_GRID_KW, ) self.long_name_bool = customtkinter.BooleanVar() self.long_name_button_title = customtkinter.StringVar( value="False", ) self.long_name_switch = customtkinter.CTkSwitch( master=self.frame_right, textvariable=self.long_name_button_title, command=self.long_name_callback, onvalue=True, offvalue=False, **KW_SWITCH, ) self.long_name_switch.deselect() self.long_name_switch.grid( row=9, column=1, ) # ============ CONFIG NAME ============ def setup_config_name(self): self.config_name_label = customtkinter.CTkLabel( text="Config Name:", **self.RIGHT_LABEL_KW, ) self.config_name_label.grid( row=10, column=0, **RIGHT_LABEL_GRID_KW, ) self.config_button = customtkinter.CTkButton( master=self.frame_right, text="Select file", command=self.config_callback, **KW_BUTTON_BASE, **KW_BUTTON_BAD_COLORS, ) self.config_button.grid( row=10, column=1, pady=12, padx=10, ) self.config_is_okay = False self.config_file_path = None # ============ OUTPUT DIRECTORY ============ def setup_output_dir(self): self.output_dir_label = customtkinter.CTkLabel( text="Output Directory", **self.RIGHT_LABEL_KW, ) self.output_dir_label.grid( row=12, column=0, **RIGHT_LABEL_GRID_KW, ) self.output_dir_button = customtkinter.CTkButton( master=self.frame_right, text=format_directory(cli_utils.output_dir_default), command=self.output_dir_callback, **KW_BUTTON_BASE, **KW_BUTTON_GOOD_COLORS, ) self.output_dir_button.grid( row=12, column=1, ) self.output_dir_path = cli_utils.output_dir_default # ============ SAVE CONFIG ============ def setup_save_config(self): self.frame_save_config = customtkinter.CTkFrame( master=self, fg_color="#212325", ) self.frame_save_config.grid( row=3, column=0, ) self.save_config_button = customtkinter.CTkButton( master=self.frame_save_config, text="Save Config", command=self.save_config_callback, ) self.save_config_button.grid( row=0, column=0, pady=12, padx=10, ) # ============ BAM FILE (FILE) ============ # def init_bam(self): def bam_callback(self): filepaths = filedialog.askopenfilenames() # filepath = filedialog.askopenfilename() if filepaths == "": return elif len(filepaths) == 1: filepath = filepaths[0] text = path_to_text(filepath) self.bam_button.configure(text=text) self.bam_file_path = [Path(filepath)] else: # self.bam_file_string.set(str(filepaths)) self.bam_button.configure(text="File paths set") self.bam_file_path = [Path(path) for path in filepaths] self.bam_is_okay = True self.bam_button.configure(**KW_BUTTON_GOOD_COLORS) # ============ DAMAGE MODE (ENUM) ============ def damage_mode_collback(self, choice): if choice == cli_utils.DAMAGE_MODE.LCA: self.damage_mode_value = cli_utils.DAMAGE_MODE.LCA elif choice == cli_utils.DAMAGE_MODE.LOCAL: self.damage_mode_value = cli_utils.DAMAGE_MODE.LOCAL elif choice == cli_utils.DAMAGE_MODE.GLOBAL: self.damage_mode_value = cli_utils.DAMAGE_MODE.GLOBAL if choice == cli_utils.DAMAGE_MODE.LCA: lca_state = "normal" text_color = "gray90" slider = KW_SLIDER lca_rank_menu_kw = KW_OPTIONS_MENU switch = KW_SWITCH self.is_lca = True else: lca_state = "disabled" text_color = "gray40" slider = KW_SLIDER_DISABLED lca_rank_menu_kw = KW_OPTIONS_MENU_DISABLED switch = KW_SWITCH_DISABLED self.is_lca = False texts = [ self.names_label, self.nodes_label, self.acc2tax_label, self.min_mapping_quality_label, self.min_mapping_quality_value, self.custom_database_label, self.lca_rank_label, ] for text in texts: text.configure(text_color=text_color) states = [ self.names_button, self.nodes_button, self.acc2tax_button, self.min_mapping_quality_slider, self.custom_database_switch, self.lca_rank_menu, ] for state in states: state.configure(state=lca_state) self.min_mapping_quality_slider.configure(**slider) self.lca_rank_menu.configure(**lca_rank_menu_kw) self.custom_database_switch.configure(**switch) if choice == cli_utils.DAMAGE_MODE.LCA: self.names_button.configure(**self.names_button_colors) self.nodes_button.configure(**self.nodes_button_colors) self.acc2tax_button.configure(**self.acc2tax_button_colors) else: self.names_button.configure(**KW_BUTTON_GOOD_COLORS) self.nodes_button.configure(**KW_BUTTON_GOOD_COLORS) self.acc2tax_button.configure(**KW_BUTTON_GOOD_COLORS) self.check_similarity_scores() # ============ NAMES FILE (FILE) ============ def names_callback(self): filepath = filedialog.askopenfilename() if filepath != "": self.names_file_path = Path(filepath) text = path_to_text(filepath) self.names_button.configure(text=text) self.names_button.configure(**KW_BUTTON_GOOD_COLORS) self.names_is_okay = True self.names_button_colors = KW_BUTTON_GOOD_COLORS # ============ NODES FILE (FILE) ============ def nodes_callback(self): filepath = filedialog.askopenfilename() if filepath != "": self.nodes_file_path = Path(filepath) text = path_to_text(filepath) self.nodes_button.configure(text=text) self.nodes_button.configure(**KW_BUTTON_GOOD_COLORS) self.nodes_is_okay = True self.nodes_button_colors = KW_BUTTON_GOOD_COLORS # ============ ACC2TAX FILE (FILE) ============ def acc2tax_callback(self): filepath = filedialog.askopenfilename() if filepath != "": self.acc2tax_file_path = Path(filepath) text = path_to_text(filepath) self.acc2tax_button.configure(text=text) self.acc2tax_button.configure(**KW_BUTTON_GOOD_COLORS) self.acc2tax_is_okay = True self.acc2tax_button_colors = KW_BUTTON_GOOD_COLORS ############# def config_callback(self): filepath = filedialog.asksaveasfilename() if filepath != "": if not ("yaml" in filepath or "yml" in filepath): filepath += ".yaml" self.config_file_path = Path(filepath) text = path_to_text(filepath) self.config_button.configure(text=text) self.config_button.configure(**KW_BUTTON_GOOD_COLORS) self.config_is_okay = True self.config_button_colors = KW_BUTTON_GOOD_COLORS # ============ MAPPING QUALITY (INTEGER) ============ def min_mapping_quality_slider_callback(self, value): self.min_mapping_quality_value.configure(text=f"= {int(value):>2d}") # ============ CUSTOM DATABASE (BOOL) ============ def custom_database_callback(self): state = self.custom_database_switch.get() self.custom_database_button_title.set(str(state)) self.custom_database_bool.set(state) # ============ LCA RANK (ENUM) ============ def lca_rank_callback(self, choice): self.lca_rank_string.set(choice if choice != "none" else cli_utils.RANKS.none) # ============ MAX POSITION (INTEGER) ============ def max_position_slider_callback(self, value): self.max_position_value.configure(text=f"= {int(value):>2d}") # ============ BAYESIAN (BOOL) ============ def bayesian_callback(self): state = self.bayesian_switch.get() self.bayesian_button_title.set(str(state)) self.bayesian_bool.set(state) # ============ FORWARD (BOOL) ============ def forward_callback(self): state = self.forward_switch.get() self.forward_button_title.set(str(state)) self.forward_bool.set(state) # ============ PARALLEL CORES (SLIDER) ============ def parallel_samples_slider_callback(self, value): self.parallel_samples_value.configure(text=f"= {int(value):>2d}") # ============ CORES PER SAMPLE (SLIDER) ============ def cores_per_sample_slider_callback(self, value): self.cores_per_sample_value.configure(text=f"= {int(value):>2d}") # ============ LONG NAME (ENTRY) ============ def long_name_callback(self): state = self.long_name_switch.get() self.long_name_button_title.set(str(state)) self.long_name_bool.set(state) # ============ CHECK SIMILARITY SCORE ============ def check_similarity_scores(self): if self.is_lca: text_color = "gray90" self.similarity_score_label.configure(text_color=text_color) self.similarity_score_to.configure(text_color=text_color) self.similarity_score_min.configure(state="normal") self.similarity_score_max.configure(state="normal") try: min_score = float(self.similarity_score_min.get()) max_score = float(self.similarity_score_max.get()) is_float = True except ValueError: is_float = False if is_float and (0 <= min_score <= max_score <= 1): self.similarity_score_min.configure(**KW_ENTRY_GOOD_COLORS) self.similarity_score_max.configure(**KW_ENTRY_GOOD_COLORS) self.similarity_is_ok = True else: self.similarity_score_min.configure(**KW_ENTRY_BAD_COLORS) self.similarity_score_max.configure(**KW_ENTRY_BAD_COLORS) self.similarity_is_ok = False else: text_color = "gray40" self.similarity_score_label.configure(text_color=text_color) self.similarity_score_to.configure(text_color=text_color) self.similarity_score_min.configure(state="disabled", **KW_ENTRY_DISABLED) self.similarity_score_max.configure(state="disabled", **KW_ENTRY_DISABLED) def check_similarity_scores_background(self, interval_sec): # run forever while True: # block for the interval sleep(interval_sec) # perform the task self.check_similarity_scores() def start_similarity_scores_background_thread(self): # create and start the daemon thread daemon = Thread( target=self.check_similarity_scores_background, args=(0.05,), daemon=True, name="Similarity-score-checking", ) daemon.start() # ============ CHECK MIN READS ============ def check_minimum_reads(self): try: min_reads = int(self.min_reads_value.get()) is_int = True except ValueError: is_int = False if is_int and (0 <= min_reads): self.min_reads_is_ok = True self.min_reads_entry.configure(**KW_ENTRY_GOOD_COLORS) else: self.min_reads_entry.configure(**KW_ENTRY_BAD_COLORS) self.min_reads_is_ok = False def check_minimum_reads_background(self, interval_sec): # run forever while True: # block for the interval sleep(interval_sec) # perform the task self.check_minimum_reads() def start_minimum_reads_background_thread(self): # create and start the daemon thread daemon = Thread( target=self.check_minimum_reads_background, args=(0.05,), daemon=True, name="minimum-reads-checking", ) daemon.start() # ============ OUTPUT DIR (DIRECTORY) ============ def output_dir_callback(self): # get a directory path by user filepath = filedialog.askdirectory() self.output_dir_path = Path(filepath) text = format_directory(Path(filepath)) self.output_dir_button.configure(text=text) def create_popup_window(self, text): window_popup = customtkinter.CTkToplevel(self) window_popup.title("metaDMG - Error") width = 365 height = 110 x, y = self.get_center_coordinates(width, height) window_popup.geometry(f"{width}x{height}+{x}+{y}") label = customtkinter.CTkLabel( window_popup, text=f"Error occurred in config creation. \nPlease {text}.", ) label.grid( row=0, column=0, padx=80, pady=12, ) def close_popup_callback(): window_popup.destroy() button = customtkinter.CTkButton( master=window_popup, text="Close", command=close_popup_callback, ) button.grid( row=1, column=0, padx=80, pady=12, ) # ============ PRINT ============ def config_is_good(self): self.check_similarity_scores() self.check_minimum_reads() if not self.bam_is_okay: self.create_popup_window("fix BAM file") return False if self.is_lca and (not self.names_is_okay): self.create_popup_window("fix names file") return False if self.is_lca and (not self.nodes_is_okay): self.create_popup_window("fix nodes file") return False if self.is_lca and (not self.acc2tax_is_okay): self.create_popup_window("fix acc2tax file") return False if self.is_lca and (not self.similarity_is_ok): self.create_popup_window("fix similarity score") return False if not self.min_reads_is_ok: self.create_popup_window("fix minimum number of reads") return False if not self.config_is_okay: self.create_popup_window("fix config file name") return False return True def get_config(self): if not self.config_is_good(): return None from metaDMG import __version__ config = cli_utils.get_config_dict( samples=self.bam_file_path, damage_mode=self.damage_mode_value, # names=self.names_file_path, nodes=self.nodes_file_path, acc2tax=self.acc2tax_file_path, min_similarity_score=float(self.similarity_score_min.get()), max_similarity_score=float(self.similarity_score_max.get()), min_edit_dist=None, max_edit_dist=None, min_mapping_quality=int(self.min_mapping_quality_slider.get()), custom_database=self.custom_database_bool.get(), lca_rank=self.lca_rank_string.get(), # metaDMG_cpp="./metaDMG-cpp", max_position=int(self.max_position_slider.get()), min_reads=int(self.min_reads_value.get()), weight_type=1, forward_only=self.forward_bool.get(), bayesian=self.bayesian_bool.get(), output_dir=self.output_dir_path, parallel_samples=int(self.parallel_samples_slider.get()), cores_per_sample=int(self.cores_per_sample_slider.get()), config_file=self.config_file_path, sample_prefix=self.prefix_entry.get(), sample_suffix=self.suffix_entry.get(), long_name=self.long_name_bool.get(), __version__=__version__, ) return config def save_config_file(self, config, overwrite_config=False): if self.verbose: print("") print("Config file to save:") print(config) cli_utils.save_config_file( config=config, config_file=self.config_file_path, overwrite_config=overwrite_config, verbose=self.verbose, ) def make_overwrite_window(self, config): window_overwrite = customtkinter.CTkToplevel(self) window_overwrite.title("metaDMG - Computing") width = 365 height = 110 x, y = self.get_center_coordinates(width, height) window_overwrite.geometry(f"{width}x{height}+{x}+{y}") label = customtkinter.CTkLabel( window_overwrite, text="Config file already exists. Do you want to overwrite it?", ) label.grid( row=0, column=0, columnspan=2, padx=20, pady=12, ) def no_overwrite_callback(): window_overwrite.destroy() def overwrite_callback(): self.save_config_file(config=config, overwrite_config=True) window_overwrite.destroy() button_yes = customtkinter.CTkButton( master=window_overwrite, text="Yes", command=overwrite_callback, ) button_yes.grid( row=1, column=0, padx=20, pady=12, ) button_no = customtkinter.CTkButton( master=window_overwrite, text="No", command=no_overwrite_callback, ) button_no.grid( row=1, column=1, padx=20, pady=12, ) def save_config_callback(self): config = self.get_config() if config is None: return if self.config_file_path.exists(): self.make_overwrite_window(config) else: self.save_config_file(config) # ============ OTHER ============ def on_closing(self, event=0): self.destroy() def get_center_coordinates(self, width, height): # get screen width and height ws = self.winfo_screenwidth() # width of the screen hs = self.winfo_screenheight() # height of the screen # calculate x and y coordinates for the Tk root window x = (ws / 2) - (width / 2) y = (hs / 2) - (height / 2) return int(x), int(y) if __name__ == "__main__": gui = Gui(verbose=True) gui.mainloop()