diff --git a/jass/__main__.py b/jass/__main__.py index 78f40102ef431e7e8fcc862e9a3022ce32f1ac59..27b0e25e5222717725f1ffe346c7efcc140e0e81 100644 --- a/jass/__main__.py +++ b/jass/__main__.py @@ -32,32 +32,32 @@ def absolute_path_of_the_file(fileName, output_file = False): if (Directory_path_exist == False): # Test the path using the Jass data directory absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName)) - + Directory_path_exist = os.path.exists(os.path.dirname(absoluteFilePath)) - + if (Directory_path_exist == False): Message = "The directory of the file {} does not exist".format(fileName) raise NameError(Message) else: # Test if the file path exist File_path_exist = os.path.exists(absoluteFilePath) - + if (File_path_exist == False): # Test the path using the Jass data directory absoluteFilePath = os.path.normpath(os.path.join(config["DATA_DIR"], fileName)) File_path_exist = os.path.exists(absoluteFilePath) - + if (File_path_exist == False): Message = "The file {} does not exist".format(fileName) raise NameError(Message) - + # Test if it is realy a file Is_a_file = os.path.isfile(absoluteFilePath) - + if (not Is_a_file) : Message = "{} is not a file".format(fileName) raise NameError(Message) - + return absoluteFilePath @@ -72,7 +72,7 @@ def w_list_phenotypes(args): def compute_worktable(args): - + csv_file_path = args.csv_file_path if (csv_file_path is not None): csv_file_path = absolute_path_of_the_file(csv_file_path, True) @@ -82,7 +82,7 @@ def compute_worktable(args): remove_nan = not (args.keep_nans) significance_treshold = float(args.significance_treshold) post_filtering = bool(args.post_filtering) - custom_loadings = args.custom_loadings + custom_loadings = args.custom_loadings chromosome = args.chromosome_number pos_Start = args.start_position pos_End = args.end_position @@ -99,10 +99,10 @@ def compute_worktable(args): strategy = args.strategy create_worktable_file( - phenotype_ids = selected_phenotypes, - init_file_path = init_table_path, + phenotype_ids = selected_phenotypes, + init_file_path = init_table_path, project_hdf_path = worktable_path, - remove_nan = remove_nan, + remove_nan = remove_nan, stat = strategy, optim_na = True, csv_file = csv_file_path, @@ -125,8 +125,8 @@ def w_create_project_data(args): manhattan_plot_path = absolute_path_of_the_file(args.manhattan_plot_path, True) quadrant_plot_path = absolute_path_of_the_file(args.quadrant_plot_path, True) create_global_plot(worktable_path, manhattan_plot_path) - create_quadrant_plot(worktable_path, - quadrant_plot_path, + create_quadrant_plot(worktable_path, + quadrant_plot_path, significance_treshold = float(args.significance_treshold)) @@ -136,7 +136,7 @@ def w_create_inittable(args): regions_map_path = absolute_path_of_the_file(args.regions_map_path) description_file_path = absolute_path_of_the_file(args.description_file_path) init_table_path = absolute_path_of_the_file(args.init_table_path, True) - + create_inittable_file( input_data_path, regions_map_path, @@ -155,8 +155,8 @@ def w_plot_quadrant(args): worktable_path = absolute_path_of_the_file(args.worktable_path) plot_path = absolute_path_of_the_file(args.plot_path) significance_treshold = float(args.significance_treshold) - create_quadrant_plot(worktable_path, - plot_path, + create_quadrant_plot(worktable_path, + plot_path, significance_treshold=significance_treshold) @@ -197,7 +197,7 @@ def get_parser(): parser_create_pd.add_argument( "--worktable-path", required=True, help="path to the worktable file to generate" ) - parser_create_pd.add_argument("--keep-nans", action="store_true", default=False) + parser_create_pd.add_argument("--keep-nans", action="store_true", default=True) parser_create_pd.add_argument( "--manhattan-plot-path", required=True, @@ -237,7 +237,7 @@ def get_parser(): required=False, help="path to the results file in csv format" ) - + parser_create_pd.add_argument( "--chromosome-number", required=False, @@ -255,7 +255,7 @@ def get_parser(): required=False, help="option used only for local analysis: end position of the region studied" ) - + strategies = parser_create_pd.add_mutually_exclusive_group() strategies.add_argument("--omnibus", action="store_true", default=True) strategies.add_argument("--sumz", action="store_true", default=False) @@ -336,15 +336,15 @@ def get_parser(): required=False, help="path to the results file in csv format" ) - + parser_create_wt.add_argument( "--chunk-size", required=False, default=50, help="Number of region to load in memory at once", ) - - parser_create_wt.add_argument("--keep-nans", action="store_true", default=False) + + parser_create_wt.add_argument("--keep-nans", action="store_true", default=True) parser_create_wt.add_argument( "--chromosome-number", @@ -363,14 +363,14 @@ def get_parser(): required=False, help="option used only for local analysis: end position of the region studied" ) - + strategies = parser_create_wt.add_mutually_exclusive_group() strategies.add_argument("--omnibus", action="store_true", default=True) strategies.add_argument("--sumz", action="store_true", default=False) strategies.add_argument("--fisher_test", action="store_true", default=False) strategies.add_argument("--meta_analysis", action="store_true", default=False) strategies.add_argument("--strategy") - + parser_create_wt.set_defaults(func=w_create_worktable) # ------- plot-manhattan ------- @@ -385,8 +385,8 @@ def get_parser(): help="path to the worktable file containing the data", ) parser_create_mp.add_argument( - "--plot-path", - required=True, + "--plot-path", + required=True, help="path to the manhattan plot file to generate" ) parser_create_mp.set_defaults(func=w_plot_manhattan) @@ -402,8 +402,8 @@ def get_parser(): help="path to the worktable file containing the data", ) parser_create_mp.add_argument( - "--plot-path", - required=True, + "--plot-path", + required=True, help="path to the quadrant plot file to generate" ) parser_create_mp.add_argument( @@ -412,7 +412,7 @@ def get_parser(): help="threshold at which a p-value is considered significant" ) parser_create_mp.set_defaults(func=w_plot_quadrant) - + return parser