gsMap 1.71.1__py3-none-any.whl → 1.72.3__py3-none-any.whl

gsMap/config.py

@@ -1,805 +1,1312 @@
-import sys
-import argparse
-import logging
-from collections import OrderedDict, namedtuple
-from dataclasses import dataclass
-from pathlib import Path
-from pprint import pprint
-from typing import Callable
-from typing import Union, Literal, Tuple, Optional, List
-from functools import wraps
-import pyfiglet
-
-from gsMap.__init__ import __version__
-
-# Global registry to hold functions
-cli_function_registry = OrderedDict()
-subcommand = namedtuple('subcommand', ['name', 'func', 'add_args_function', 'description'])
-
-
-def get_gsMap_logger(logger_name):
-    logger = logging.getLogger(logger_name)
-    logger.setLevel(logging.DEBUG)
-    handler = logging.StreamHandler()
-    handler.setFormatter(logging.Formatter(
-        '[{asctime}] {levelname:.5s} | {name} - {message}', style='{'))
-    logger.addHandler(handler)
-    return logger
-
-logger = get_gsMap_logger('gsMap')
-
-# Decorator to register functions for cli parsing
-def register_cli(name: str, description: str, add_args_function: Callable) -> Callable:
-    def decorator(func: Callable) -> Callable:
-        def wrapper(*args, **kwargs):
-            name.replace('_', ' ')
-            gsMap_main_logo = pyfiglet.figlet_format("gsMap", font='doom', width=80, justify='center', ).rstrip()
-            print(gsMap_main_logo, flush=True)
-            version_number = 'Version: ' + __version__
-            print(version_number.center(80), flush=True)
-            print('=' * 80, flush=True)
-            logger.info(f"Running {name}...")
-            func(*args, **kwargs)
-            logger.info(f"Finished running {name}.")
-
-        cli_function_registry[name] = subcommand(name=name, func=wrapper, add_args_function=add_args_function,
-                                                 description=description)
-        return wrapper
-
-    return decorator
-
-def add_shared_args(parser):
-    parser.add_argument('--workdir', type=str, required=True, help='Path to the working directory.')
-    parser.add_argument('--sample_name', type=str, required=True, help='Name of the sample.')
-
-def add_find_latent_representations_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--input_hdf5_path', required=True, type=str, help='Path to the input HDF5 file.')
-    parser.add_argument('--annotation', required=True, type=str, help='Name of the annotation in adata.obs to use.')
-    parser.add_argument('--data_layer', type=str, default='counts', required=True,
-                        help='Data layer for gene expression (e.g., "count", "counts", "log1p").')
-    parser.add_argument('--epochs', type=int, default=300, help='Number of training epochs.')
-    parser.add_argument('--feat_hidden1', type=int, default=256, help='Neurons in the first hidden layer.')
-    parser.add_argument('--feat_hidden2', type=int, default=128, help='Neurons in the second hidden layer.')
-    parser.add_argument('--gat_hidden1', type=int, default=64, help='Units in the first GAT hidden layer.')
-    parser.add_argument('--gat_hidden2', type=int, default=30, help='Units in the second GAT hidden layer.')
-    parser.add_argument('--p_drop', type=float, default=0.1, help='Dropout rate.')
-    parser.add_argument('--gat_lr', type=float, default=0.001, help='Learning rate for the GAT.')
-    parser.add_argument('--n_neighbors', type=int, default=11, help='Number of neighbors for GAT.')
-    parser.add_argument('--n_comps', type=int, default=300, help='Number of principal components for PCA.')
-    parser.add_argument('--weighted_adj', action='store_true', help='Use weighted adjacency in GAT.')
-    parser.add_argument('--convergence_threshold', type=float, default=1e-4, help='Threshold for convergence.')
-    parser.add_argument('--hierarchically', action='store_true', help='Enable hierarchical latent representation finding.')
-
-
-def chrom_choice(value):
-    if value.isdigit():
-        ivalue = int(value)
-        if 1 <= ivalue <= 22:
-            return ivalue
-    elif value.lower() == 'all':
-        return value
-    else:
-        raise argparse.ArgumentTypeError(f"'{value}' is an invalid chromosome choice. Choose from 1-22 or 'all'.")
-
-
-def filter_args_for_dataclass(args_dict, data_class: dataclass):
-    return {k: v for k, v in args_dict.items() if k in data_class.__dataclass_fields__}
-
-
-def get_dataclass_from_parser(args: argparse.Namespace, data_class: dataclass):
-    remain_kwargs = filter_args_for_dataclass(vars(args), data_class)
-    print(f'Using the following arguments for {data_class.__name__}:', flush=True)
-    pprint(remain_kwargs, indent=4)
-    sys.stdout.flush()
-    return data_class(**remain_kwargs)
-
-
-def add_latent_to_gene_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--annotation', type=str, help='Name of the annotation in adata.obs to use. (optional).')
-    parser.add_argument('--no_expression_fraction', action='store_true', help='Skip expression fraction filtering.')
-    parser.add_argument('--latent_representation', type=str, choices=['latent_GVAE', 'latent_PCA'], default='latent_GVAE',
-                        help='Type of latent representation.')
-    parser.add_argument('--num_neighbour', type=int, default=21, help='Number of neighbors.')
-    parser.add_argument('--num_neighbour_spatial', type=int, default=101, help='Number of spatial neighbors.')
-    # parser.add_argument('--species', type=str, help='Species name for homolog gene mapping (optional).')
-    parser.add_argument('--homolog_file', type=str, help='Path to homologous gene conversion file (optional).')
-
-
-def add_generate_ldscore_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--chrom', type=str, required=True, help='Chromosome id (1-22) or "all".')
-    parser.add_argument('--bfile_root', type=str, required=True, help='Root path for genotype plink bfiles (.bim, .bed, .fam).')
-    parser.add_argument('--keep_snp_root', type=str, required=True, help='Root path for SNP files.')
-    parser.add_argument('--gtf_annotation_file', type=str, required=True, help='Path to GTF annotation file.')
-    parser.add_argument('--gene_window_size', type=int, default=50000, help='Gene window size in base pairs.')
-    parser.add_argument('--enhancer_annotation_file', type=str, help='Path to enhancer annotation file (optional).')
-    parser.add_argument('--snp_multiple_enhancer_strategy', type=str, choices=['max_mkscore', 'nearest_TSS'], default='max_mkscore',
-                        help='Strategy for handling multiple enhancers per SNP.')
-    parser.add_argument('--gene_window_enhancer_priority', type=str, choices=['gene_window_first', 'enhancer_first', 'enhancer_only'],
-                        help='Priority between gene window and enhancer annotations.')
-    parser.add_argument('--spots_per_chunk', type=int, default=1000, help='Number of spots per chunk.')
-    parser.add_argument('--ld_wind', type=int, default=1, help='LD window size.')
-    parser.add_argument('--ld_unit', type=str, choices=['SNP', 'KB', 'CM'], default='CM', help='Unit for LD window.')
-    parser.add_argument('--additional_baseline_annotation', type=str, default=None, help='Path of additional baseline annotations')
-
-
-def add_latent_to_gene_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--annotation', type=str, required=True, help='Name of the annotation layer.')
-    parser.add_argument('--no_expression_fraction', action='store_true', help='Skip expression fraction filtering.')
-    parser.add_argument('--latent_representation', type=str, choices=['latent_GVAE', 'latent_PCA'], default='latent_GVAE',
-                        help='Type of latent representation.')
-    parser.add_argument('--num_neighbour', type=int, default=21, help='Number of neighbors.')
-    parser.add_argument('--num_neighbour_spatial', type=int, default=101, help='Number of spatial neighbors.')
-    # parser.add_argument('--species', type=str, help='Species name for homolog gene mapping (optional).')
-    parser.add_argument('--homolog_file', type=str, help='Path to homologous gene conversion file (optional).')
-
-
-def add_spatial_ldsc_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--sumstats_file', type=str, required=True, help='Path to GWAS summary statistics file.')
-    parser.add_argument('--w_file', type=str, required=True, help='Path to regression weight file.')
-    parser.add_argument('--trait_name', type=str, required=True, help='Name of the trait being analyzed.')
-    parser.add_argument('--n_blocks', type=int, default=200, help='Number of blocks for jackknife resampling.')
-    parser.add_argument('--chisq_max', type=int, help='Maximum chi-square value for filtering SNPs.')
-    parser.add_argument('--num_processes', type=int, default=4, help='Number of processes for parallel computing.')
-    parser.add_argument('--use_additional_baseline_annotation', type=bool, nargs='?', const=True, default=True, help='Use additional baseline annotations when provided')
-
-
-def add_Cauchy_combination_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--trait_name', type=str, required=True, help='Name of the trait being analyzed.')
-    parser.add_argument('--annotation', type=str, required=True, help='Name of the annotation in adata.obs to use.')
-    parser.add_argument('--meta', type=str, help='Optional meta information.')
-    parser.add_argument('--slide', type=str, help='Optional slide information.')
-
-
-def add_report_args(parser):
-    add_shared_args(parser)
-    parser.add_argument('--trait_name', type=str, required=True, help='Name of the trait to generate the report for.')
-    parser.add_argument('--annotation', type=str, required=True, help='Annotation layer name.')
-    # parser.add_argument('--plot_type', type=str, choices=['manhattan', 'GSS', 'gsMap', 'all'], default='all',
-    #                     help="Type of diagnostic plot to generate. Choose from 'manhattan', 'GSS', 'gsMap', or 'all'.")
-    parser.add_argument('--top_corr_genes', type=int, default=50,
-                        help='Number of top correlated genes to display.')
-    parser.add_argument('--selected_genes', type=str, nargs='*',
-                        help='List of specific genes to include in the report (optional).')
-    parser.add_argument('--sumstats_file', type=str, required=True, help='Path to GWAS summary statistics file.')
-
-    # Optional arguments for customization
-    parser.add_argument('--fig_width', type=int, default=None, help='Width of the generated figures in pixels.')
-    parser.add_argument('--fig_height', type=int, default=None, help='Height of the generated figures in pixels.')
-    parser.add_argument('--point_size', type=int, default=None, help='Point size for the figures.')
-    parser.add_argument('--fig_style', type=str, default='light', choices=['dark', 'light'],
-                        help='Style of the generated figures.')
-
-def add_format_sumstats_args(parser):
-    # Required arguments
-    parser.add_argument('--sumstats', required=True, type=str,
-                        help='Path to gwas summary data')
-    parser.add_argument('--out', required=True, type=str,
-                        help='Path to save the formatted gwas data')
-
-    # Arguments for specify column name
-    parser.add_argument('--snp', default=None, type=str,
-                        help="Name of snp column (if not a name that gsMap understands)")
-    parser.add_argument('--a1', default=None, type=str,
-                        help="Name of effect allele column (if not a name that gsMap understands)")
-    parser.add_argument('--a2', default=None, type=str,
-                        help="Name of none-effect allele column (if not a name that gsMap understands)")
-    parser.add_argument('--info', default=None, type=str,
-                        help="Name of info column (if not a name that gsMap understands)")
-    parser.add_argument('--beta', default=None, type=str,
-                        help="Name of gwas beta column (if not a name that gsMap understands).")
-    parser.add_argument('--se', default=None, type=str,
-                        help="Name of gwas standar error of beta column (if not a name that gsMap understands)")
-    parser.add_argument('--p', default=None, type=str,
-                        help="Name of p-value column (if not a name that gsMap understands)")
-    parser.add_argument('--frq', default=None, type=str,
-                        help="Name of A1 ferquency column (if not a name that gsMap understands)")
-    parser.add_argument('--n', default=None, type=str,
-                        help="Name of sample size column (if not a name that gsMap understands)")
-    parser.add_argument('--z', default=None, type=str,
-                        help="Name of gwas Z-statistics column (if not a name that gsMap understands)")
-    parser.add_argument('--OR', default=None, type=str,
-                        help="Name of gwas OR column (if not a name that gsMap understands)")
-    parser.add_argument('--se_OR', default=None, type=str,
-                        help="Name of standar error of OR column (if not a name that gsMap understands)")
-
-    # Arguments for convert SNP (chr, pos) to rsid
-    parser.add_argument('--chr', default="Chr", type=str,
-                        help="Name of SNP chromosome column (if not a name that gsMap understands)")
-    parser.add_argument('--pos', default="Pos", type=str,
-                        help="Name of SNP positions column (if not a name that gsMap understands)")
-    parser.add_argument('--dbsnp', default=None, type=str,
-                        help='Path to reference dnsnp file')
-    parser.add_argument('--chunksize', default=1e+6, type=int,
-                        help='Chunk size for loading dbsnp file')
-
-    # Arguments for output format and quality
-    parser.add_argument('--format', default='gsMap', type=str,
-                        help='Format of output data', choices=['gsMap', 'COJO'])
-    parser.add_argument('--info_min', default=0.9, type=float,
-                        help='Minimum INFO score.')
-    parser.add_argument('--maf_min', default=0.01, type=float,
-                        help='Minimum MAF.')
-    parser.add_argument('--keep_chr_pos', action='store_true', default=False,
-                        help='Keep SNP chromosome and position columns in the output data')
-
-def add_run_all_mode_args(parser):
-    add_shared_args(parser)
-
-    # Required paths and configurations
-    parser.add_argument('--gsMap_resource_dir', type=str, required=True,
-                        help='Directory containing gsMap resources (e.g., genome annotations, LD reference panel, etc.).')
-    parser.add_argument('--hdf5_path', type=str, required=True,
-                        help='Path to the input spatial transcriptomics data (H5AD format).')
-    parser.add_argument('--annotation', type=str, required=True,
-                        help='Name of the annotation in adata.obs to use.')
-    parser.add_argument('--data_layer', type=str, default='counts', required=True,
-                        help='Data layer for gene expression (e.g., "count", "counts", "log1p").')
-
-    # GWAS Data Parameters
-    parser.add_argument('--trait_name', type=str, help='Name of the trait for GWAS analysis (required if sumstats_file is provided).')
-    parser.add_argument('--sumstats_file', type=str,
-                        help='Path to GWAS summary statistics file. Either sumstats_file or sumstats_config_file is required.')
-    parser.add_argument('--sumstats_config_file', type=str,
-                        help='Path to GWAS summary statistics config file. Either sumstats_file or sumstats_config_file is required.')
-
-    # Homolog Data Parameters
-    parser.add_argument('--homolog_file', type=str,
-                        help='Path to homologous gene for converting gene names from different species to human (optional, used for cross-species analysis).')
-
-    # Maximum number of processes
-    parser.add_argument('--max_processes', type=int, default=10,
-                        help='Maximum number of processes for parallel execution.')
-
-    # # Optional paths for customization
-    # parser.add_argument('--bfile_root', type=str,
-    #                     help='Root path to PLINK bfiles (LD reference panel). If not provided, it will use the default in gsMap_resource_dir.')
-    # parser.add_argument('--keep_snp_root', type=str,
-    #                     help='Root path for SNP filtering. If not provided, it will use the default in gsMap_resource_dir.')
-    # parser.add_argument('--w_file', type=str,
-    #                     help='Path to the regression weight file. If not provided, it will use the default in gsMap_resource_dir.')
-    # parser.add_argument('--snp_gene_weight_adata_path', type=str,
-    #                     help='Path to the SNP-gene weight matrix file. If not provided, it will use the default in gsMap_resource_dir.')
-    # parser.add_argument('--baseline_annotation_dir', type=str,
-    #                     help='Directory containing the baseline annotations for quick mode. If not provided, it will use the default in gsMap_resource_dir.')
-    # parser.add_argument('--SNP_gene_pair_dir', type=str,
-    #                     help='Directory for SNP-gene pair data. If not provided, it will use the default in gsMap_resource_dir.')
-
-
-def ensure_path_exists(func):
-    @wraps(func)
-    def wrapper(*args, **kwargs):
-        result = func(*args, **kwargs)
-        if isinstance(result, Path):
-            if result.suffix:
-                result.parent.mkdir(parents=True, exist_ok=True, mode=0o755)
-            else:  # It's a directory path
-                result.mkdir(parents=True, exist_ok=True, mode=0o755)
-        return result
-
-    return wrapper
-
-
-@dataclass
-class ConfigWithAutoPaths:
-    workdir: str
-    sample_name: str
-
-    def __post_init__(self):
-        if self.workdir is None:
-            raise ValueError('workdir must be provided.')
-
-    @property
-    @ensure_path_exists
-    def hdf5_with_latent_path(self) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/find_latent_representations/{self.sample_name}_add_latent.h5ad')
-
-    @property
-    @ensure_path_exists
-    def mkscore_feather_path(self) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/latent_to_gene/{self.sample_name}_gene_marker_score.feather')
-
-    @property
-    @ensure_path_exists
-    def ldscore_save_dir(self) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/generate_ldscore')
-
-    @property
-    @ensure_path_exists
-    def ldsc_save_dir(self) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/spatial_ldsc')
-
-    @property
-    @ensure_path_exists
-    def cauchy_save_dir(self) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/cauchy_combination')
-
-    @ensure_path_exists
-    def get_report_dir(self, trait_name: str) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/report/{trait_name}')
-
-    def get_gsMap_report_file(self, trait_name: str) -> Path:
-        return self.get_report_dir(trait_name) / f'{self.sample_name}_{trait_name}_gsMap_Report.html'
-
-    @ensure_path_exists
-    def get_manhattan_html_plot_path(self, trait_name: str) -> Path:
-        return Path(
-            f'{self.workdir}/{self.sample_name}/report/{trait_name}/manhattan_plot/{self.sample_name}_{trait_name}_Diagnostic_Manhattan_Plot.html')
-
-    @ensure_path_exists
-    def get_GSS_plot_dir(self, trait_name: str) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/report/{trait_name}/GSS_plot')
-
-    def get_GSS_plot_select_gene_file(self, trait_name: str) -> Path:
-        return self.get_GSS_plot_dir(trait_name) / 'plot_genes.csv'
-
-    @ensure_path_exists
-    def get_ldsc_result_file(self, trait_name: str) -> Path:
-        return Path(f'{self.ldsc_save_dir}/{self.sample_name}_{trait_name}.csv.gz')
-
-    @ensure_path_exists
-    def get_cauchy_result_file(self, trait_name: str) -> Path:
-        return Path(f'{self.cauchy_save_dir}/{self.sample_name}_{trait_name}.Cauchy.csv.gz')
-
-    @ensure_path_exists
-    def get_gene_diagnostic_info_save_path(self, trait_name: str) -> Path:
-        return Path(
-            f'{self.workdir}/{self.sample_name}/report/{trait_name}/{self.sample_name}_{trait_name}_Gene_Diagnostic_Info.csv')
-
-    @ensure_path_exists
-    def get_gsMap_plot_save_dir(self, trait_name: str) -> Path:
-        return Path(f'{self.workdir}/{self.sample_name}/report/{trait_name}/gsMap_plot')
-
-    def get_gsMap_html_plot_save_path(self, trait_name: str) -> Path:
-        return self.get_gsMap_plot_save_dir(trait_name) / f'{self.sample_name}_{trait_name}_gsMap_plot.html'
-
-@dataclass
-class FindLatentRepresentationsConfig(ConfigWithAutoPaths):
-    input_hdf5_path: str
-    # output_hdf5_path: str
-    annotation: str = None
-    data_layer: str = None
-
-    epochs: int = 300
-    feat_hidden1: int = 256
-    feat_hidden2: int = 128
-    feat_cell: int = 3000
-    gat_hidden1: int = 64
-    gat_hidden2: int = 30
-    p_drop: float = 0.1
-    gat_lr: float = 0.001
-    gcn_decay: float = 0.01
-    n_neighbors: int = 11
-    label_w: float = 1
-    rec_w: float = 1
-    input_pca: bool = True
-    n_comps: int = 300
-    weighted_adj: bool = False
-    nheads: int = 3
-    var: bool = False
-    convergence_threshold: float = 1e-4
-    hierarchically: bool = False
-
-    def __post_init__(self):
-        # self.output_hdf5_path = self.hdf5_with_latent_path
-        if self.hierarchically:
-            if self.annotation is None:
-                raise ValueError('annotation must be provided if hierarchically is True.')
-            logger.info(
-                f'------Hierarchical mode is enabled. This will find the latent representations within each annotation.')
-
-        # remind for not providing annotation
-        if self.annotation is None:
-            logger.warning(
-                'annotation is not provided. This will find the latent representations for the whole dataset.')
-        else:
-            logger.info(f'------Find latent representations for {self.annotation}...')
-
-
-@dataclass
-class LatentToGeneConfig(ConfigWithAutoPaths):
-    # input_hdf5_with_latent_path: str
-    # output_feather_path: str
-    no_expression_fraction: bool = False
-    latent_representation: str = 'latent_GVAE'
-    num_neighbour: int = 21
-    num_neighbour_spatial: int = 101
-    homolog_file: str = None
-    gM_slices: str = None
-    annotation: str = None
-
-    def __post_init__(self):
-        if self.homolog_file is not None:
-            logger.info(f"User provided homolog file to map gene names to human: {self.homolog_file}")
-            # check the format of the homolog file
-            with open(self.homolog_file, 'r') as f:
-                first_line = f.readline().strip()
-                _n_col = len(first_line.split())
-                if _n_col != 2:
-                    raise ValueError(
-                        f"Invalid homolog file format. Expected 2 columns, first column should be other species gene name, second column should be human gene name. "
-                        f"Got {_n_col} columns in the first line.")
-                else:
-                    first_col_name, second_col_name = first_line.split()
-                    self.species = first_col_name
-                    logger.info(
-                        f"Homolog file provided and will map gene name from column1:{first_col_name} to column2:{second_col_name}")
-        else:
-            logger.info("No homolog file provided. Run in human mode.")
-
-
-@dataclass
-class GenerateLDScoreConfig(ConfigWithAutoPaths):
-    chrom: Union[int, str]
-
-    bfile_root: str
-    keep_snp_root: Optional[str]
-
-    # annotation by gene distance
-    gtf_annotation_file: str
-    gene_window_size: int = 50000
-
-    # annotation by enhancer
-    enhancer_annotation_file: str = None
-    snp_multiple_enhancer_strategy: Literal['max_mkscore', 'nearest_TSS'] = 'max_mkscore'
-    gene_window_enhancer_priority: Optional[Literal['gene_window_first', 'enhancer_first', 'enhancer_only',]] = None
-
-    # for calculating ld score
-    additional_baseline_annotation: str = None
-    spots_per_chunk: int = 1_000
-    ld_wind: int = 1
-    ld_unit: str = 'CM'
-
-    # zarr config
-    ldscore_save_format: Literal['feather', 'zarr', 'quick_mode'] = 'feather'
-
-    zarr_chunk_size: Tuple[int, int] = None
-
-    # for pre calculating the SNP Gene ldscore Weight
-    save_pre_calculate_snp_gene_weight_matrix: bool = False
-
-    baseline_annotation_dir: Optional[str] = None
-    SNP_gene_pair_dir: Optional[str] = None
-    def __post_init__(self):
-        # if self.mkscore_feather_file is None:
-        #     self.mkscore_feather_file = self._get_mkscore_feather_path()
-
-        if self.enhancer_annotation_file is not None and self.gene_window_enhancer_priority is None:
-            logger.warning("enhancer_annotation_file is provided but gene_window_enhancer_priority is not provided. "
-                           "by default, gene_window_enhancer_priority is set to 'enhancer_only', when enhancer_annotation_file is provided.")
-            self.gene_window_enhancer_priority = 'enhancer_only'
-        if self.enhancer_annotation_file is None and self.gene_window_enhancer_priority is not None:
-            logger.warning("gene_window_enhancer_priority is provided but enhancer_annotation_file is not provided. "
-                           "by default, gene_window_enhancer_priority is set to None, when enhancer_annotation_file is not provided.")
-            self.gene_window_enhancer_priority = None
-        assert self.gene_window_enhancer_priority in [None, 'gene_window_first', 'enhancer_first', 'enhancer_only', ], \
-            f"gene_window_enhancer_priority must be one of None, 'gene_window_first', 'enhancer_first', 'enhancer_only', but got {self.gene_window_enhancer_priority}."
-        if self.gene_window_enhancer_priority in ['gene_window_first', 'enhancer_first']:
-            logger.info(f'Both gene_window and enhancer annotation will be used to calculate LD score. ')
-            logger.info(
-                f'SNP within +-{self.gene_window_size} bp of gene body will be used and enhancer annotation will be used to calculate LD score. If a snp maps to multiple enhancers, the strategy to choose by your select strategy: {self.snp_multiple_enhancer_strategy}.')
-        elif self.gene_window_enhancer_priority == 'enhancer_only':
-            logger.info(f'Only enhancer annotation will be used to calculate LD score. ')
-        else:
-            logger.info(
-                f'Only gene window annotation will be used to calculate LD score. SNP within +-{self.gene_window_size} bp of gene body will be used. ')
-
-        # remind for baseline annotation
-        if self.additional_baseline_annotation is None:
-            logger.info(f'------Baseline annotation is not provided. Default baseline annotation will be used.')
-        else:
-            logger.info(
-                f'------Baseline annotation is provided. Additional baseline annotation will be used with the default baseline annotation.')
-            logger.info(f'------Baseline annotation directory: {self.additional_baseline_annotation}')
-            # check the existence of baseline annotation
-            if self.chrom == 'all':
-                for chrom in range(1, 23):
-                    chrom = str(chrom)
-                    baseline_annotation_path = Path(
-                        self.additional_baseline_annotation) / f'baseline.{chrom}.annot.gz'
-                    if not baseline_annotation_path.exists():
-                        raise FileNotFoundError(
-                            f'baseline.{chrom}.annot.gz is not found in {self.additional_baseline_annotation}.')
-            else:
-                baseline_annotation_path = Path(
-                    self.additional_baseline_annotation) / f'baseline.{self.chrom}.annot.gz'
-                if not baseline_annotation_path.exists():
-                    raise FileNotFoundError(
-                        f'baseline.{self.chrom}.annot.gz is not found in {self.additional_baseline_annotation}.')
-
-        # set the default zarr chunk size
-        if self.ldscore_save_format == 'zarr' and self.zarr_chunk_size is None:
-            self.zarr_chunk_size = (10_000, self.spots_per_chunk)
-
-
-@dataclass
-class SpatialLDSCConfig(ConfigWithAutoPaths):
-    w_file: str
-    # ldscore_save_dir: str
-    use_additional_baseline_annotation: bool = True
-    trait_name: Optional[str] = None
-    sumstats_file: Optional[str] = None
-    sumstats_config_file: Optional[str] = None
-    num_processes: int = 4
-    not_M_5_50: bool = False
-    n_blocks: int = 200
-    chisq_max: Optional[int] = None
-    all_chunk: Optional[int] = None
-    chunk_range: Optional[Tuple[int, int]] = None
-
-    ldscore_save_format: Literal['feather', 'zarr', 'quick_mode'] = 'feather'
-
-    spots_per_chunk_quick_mode: int = 1_000
-    snp_gene_weight_adata_path: Optional[str] = None
-
-    def __post_init__(self):
-        super().__post_init__()
-        if self.sumstats_file is None and self.sumstats_config_file is None:
-            raise ValueError('One of sumstats_file and sumstats_config_file must be provided.')
-        if self.sumstats_file is not None and self.sumstats_config_file is not None:
-            raise ValueError('Only one of sumstats_file and sumstats_config_file must be provided.')
-        if self.sumstats_file is not None and self.trait_name is None:
-            raise ValueError('trait_name must be provided if sumstats_file is provided.')
-        if self.sumstats_config_file is not None and self.trait_name is not None:
-            raise ValueError('trait_name must not be provided if sumstats_config_file is provided.')
-        self.sumstats_config_dict = {}
-        # load the sumstats config file
-        if self.sumstats_config_file is not None:
-            import yaml
-            with open(self.sumstats_config_file) as f:
-                config = yaml.load(f, Loader=yaml.FullLoader)
-            for trait_name, sumstats_file in config.items():
-                assert Path(sumstats_file).exists(), f'{sumstats_file} does not exist.'
-        # load the sumstats file
-        elif self.sumstats_file is not None:
-            self.sumstats_config_dict[self.trait_name] = self.sumstats_file
-        else:
-            raise ValueError('One of sumstats_file and sumstats_config_file must be provided.')
-
-        for sumstats_file in self.sumstats_config_dict.values():
-            assert Path(sumstats_file).exists(), f'{sumstats_file} does not exist.'
-
-        # check if additional baseline annotation is exist
-        # self.use_additional_baseline_annotation = False
-        
-        if self.use_additional_baseline_annotation:
-            self.process_additional_baseline_annotation()
-
-    def process_additional_baseline_annotation(self):
-        additional_baseline_annotation = Path(self.ldscore_save_dir) / 'additional_baseline'
-        dir_exists = additional_baseline_annotation.exists()
-
-        if not dir_exists:
-            self.use_additional_baseline_annotation = False
-            # if self.use_additional_baseline_annotation:
-            #     logger.warning(f"additional_baseline directory is not found in {self.ldscore_save_dir}.")
-            #     print('''\
-            #         if you want to use additional baseline annotation, 
-            #         please provide additional baseline annotation when calculating ld score.
-            #         ''')
-            #     raise FileNotFoundError(
-            #         f'additional_baseline directory is not found.')
-            # return
-            # self.use_additional_baseline_annotation = self.use_additional_baseline_annotation or True
-        else:
-            logger.info(
-                f'------Additional baseline annotation is provided. It will be used with the default baseline annotation.')
-            logger.info(f'------Additional baseline annotation directory: {additional_baseline_annotation}')
-
-            chrom_list = range(1, 23)
-            for chrom in chrom_list:
-                baseline_annotation_path = additional_baseline_annotation / f'baseline.{chrom}.l2.ldscore.feather'
-                if not baseline_annotation_path.exists():
-                    raise FileNotFoundError(
-                        f'baseline.{chrom}.annot.gz is not found in {additional_baseline_annotation}.')
-        return None
-
-
-@dataclass
-class CauchyCombinationConfig(ConfigWithAutoPaths):
-    trait_name: str
-    annotation: str
-    meta: str = None
-    slide: str = None
-
-
-@dataclass
-class VisualizeConfig(ConfigWithAutoPaths):
-    trait_name: str
-
-    annotation: str = None
-    fig_title: str = None
-    fig_height: int = 600
-    fig_width: int = 800
-    point_size: int = None
-    fig_style: Literal['dark', 'light'] = 'light'
-
-
-@dataclass
-class DiagnosisConfig(ConfigWithAutoPaths):
-    annotation: str
-    # mkscore_feather_file: str
-
-    trait_name: str
-    sumstats_file: str
-    plot_type: Literal['manhattan', 'GSS', 'gsMap', 'all'] = 'all'
-    top_corr_genes: int = 50
-    selected_genes: Optional[List[str]] = None
-
-    fig_width: Optional[int] = None
-    fig_height: Optional[int] = None
-    point_size: Optional[int] = None
-    fig_style: Literal['dark', 'light'] = 'light'
-
-    def __post_init__(self):
-        if any([self.fig_width, self.fig_height, self.point_size]):
-            logger.info('Customizing the figure size and point size.')
-            assert all([self.fig_width, self.fig_height, self.point_size]), 'All of fig_width, fig_height, and point_size must be provided.'
-            self.customize_fig = True
-        else:
-            self.customize_fig = False
-@dataclass
-class ReportConfig(DiagnosisConfig):
-    pass
-
-
-@dataclass
-class RunAllModeConfig(ConfigWithAutoPaths):
-    gsMap_resource_dir: str
-
-    # == ST DATA PARAMETERS ==
-    hdf5_path: str
-    annotation: str
-    data_layer: str = 'X'
-
-    # ==GWAS DATA PARAMETERS==
-    trait_name: Optional[str] = None
-    sumstats_file: Optional[str] = None
-    sumstats_config_file: Optional[str] = None
-
-    # === homolog PARAMETERS ===
-    homolog_file: Optional[str] = None
-
-    max_processes: int = 10
-
-    def __post_init__(self):
-        super().__post_init__()
-        self.gtffile = f"{self.gsMap_resource_dir}/genome_annotation/gtf/gencode.v39lift37.annotation.gtf"
-        self.bfile_root = f"{self.gsMap_resource_dir}/LD_Reference_Panel/1000G_EUR_Phase3_plink/1000G.EUR.QC"
-        self.keep_snp_root = f"{self.gsMap_resource_dir}/LDSC_resource/hapmap3_snps/hm"
-        self.w_file = f"{self.gsMap_resource_dir}/LDSC_resource/weights_hm3_no_hla/weights."
-        self.snp_gene_weight_adata_path = f"{self.gsMap_resource_dir}/quick_mode/snp_gene_weight_matrix.h5ad"
-        self.baseline_annotation_dir = Path(f"{self.gsMap_resource_dir}/quick_mode/baseline").resolve()
-        self.SNP_gene_pair_dir = Path(f"{self.gsMap_resource_dir}/quick_mode/SNP_gene_pair").resolve()
-        # check the existence of the input files and resources files
-        for file in [self.hdf5_path, self.gtffile]:
-            if not Path(file).exists():
-                raise FileNotFoundError(f"File {file} does not exist.")
-
-        if self.sumstats_file is None and self.sumstats_config_file is None:
-            raise ValueError('One of sumstats_file and sumstats_config_file must be provided.')
-        if self.sumstats_file is not None and self.sumstats_config_file is not None:
-            raise ValueError('Only one of sumstats_file and sumstats_config_file must be provided.')
-        if self.sumstats_file is not None and self.trait_name is None:
-            raise ValueError('trait_name must be provided if sumstats_file is provided.')
-        if self.sumstats_config_file is not None and self.trait_name is not None:
-            raise ValueError('trait_name must not be provided if sumstats_config_file is provided.')
-        self.sumstats_config_dict = {}
-        # load the sumstats config file
-        if self.sumstats_config_file is not None:
-            import yaml
-            with open(self.sumstats_config_file) as f:
-                config = yaml.load(f, Loader=yaml.FullLoader)
-            for trait_name, sumstats_file in config.items():
-                assert Path(sumstats_file).exists(), f'{sumstats_file} does not exist.'
-                self.sumstats_config_dict[trait_name] = sumstats_file
-        # load the sumstats file
-        elif self.sumstats_file is not None and self.trait_name is not None:
-            self.sumstats_config_dict[self.trait_name] = self.sumstats_file
-        else:
-            raise ValueError('One of sumstats_file and sumstats_config_file must be provided.')
-
-        for sumstats_file in self.sumstats_config_dict.values():
-            assert Path(sumstats_file).exists(), f'{sumstats_file} does not exist.'
-
-
-@dataclass
-class FormatSumstatsConfig:
-    sumstats: str
-    out: str
-    dbsnp: str
-    snp: str = None
-    a1: str = None
-    a2: str = None
-    info: str = None
-    beta: str = None
-    se: str = None
-    p: str = None
-    frq: str = None
-    n: str = None
-    z: str = None
-    OR: str = None
-    se_OR: str = None
-    format: str = None
-    chr: str = None
-    pos: str = None
-    chunksize: int = 1e+7
-    info_min: float = 0.9
-    maf_min: float = 0.01
-    keep_chr_pos: bool = False
-
-
-@register_cli(name='run_find_latent_representations',
-              description='Run Find_latent_representations \nFind the latent representations of each spot by running GNN-VAE',
-              add_args_function=add_find_latent_representations_args)
-def run_find_latent_representation_from_cli(args: argparse.Namespace):
-    from gsMap.find_latent_representation import run_find_latent_representation
-    config = get_dataclass_from_parser(args, FindLatentRepresentationsConfig)
-    run_find_latent_representation(config)
-
-
-@register_cli(name='run_latent_to_gene',
-              description='Run Latent_to_gene \nEstimate gene marker gene scores for each spot by using latent representations from nearby spots',
-              add_args_function=add_latent_to_gene_args)
-def run_latent_to_gene_from_cli(args: argparse.Namespace):
-    from gsMap.latent_to_gene import run_latent_to_gene
-    config = get_dataclass_from_parser(args, LatentToGeneConfig)
-    run_latent_to_gene(config)
-
-
-@register_cli(name='run_generate_ldscore',
-              description='Run Generate_ldscore \nGenerate LD scores for each spot',
-              add_args_function=add_generate_ldscore_args)
-def run_generate_ldscore_from_cli(args: argparse.Namespace):
-    from gsMap.generate_ldscore import run_generate_ldscore
-    config = get_dataclass_from_parser(args, GenerateLDScoreConfig)
-    run_generate_ldscore(config)
-
-
-@register_cli(name='run_spatial_ldsc',
-              description='Run Spatial_ldsc \nRun spatial LDSC for each spot',
-              add_args_function=add_spatial_ldsc_args)
-def run_spatial_ldsc_from_cli(args: argparse.Namespace):
-    from gsMap.spatial_ldsc_multiple_sumstats import run_spatial_ldsc
-    config = get_dataclass_from_parser(args, SpatialLDSCConfig)
-    run_spatial_ldsc(config)
-
-
-@register_cli(name='run_cauchy_combination',
-              description='Run Cauchy_combination for each annotation',
-              add_args_function=add_Cauchy_combination_args)
-def run_Cauchy_combination_from_cli(args: argparse.Namespace):
-    from gsMap.cauchy_combination_test import run_Cauchy_combination
-    config = get_dataclass_from_parser(args, CauchyCombinationConfig)
-    run_Cauchy_combination(config)
-
-
-@register_cli(name='run_report',
-              description='Run Report to generate diagnostic plots and tables',
-              add_args_function=add_report_args)
-def run_Report_from_cli(args: argparse.Namespace):
-    from gsMap.report import run_report
-    config = get_dataclass_from_parser(args, ReportConfig)
-    run_report(config)
-
-
-@register_cli(name='format_sumstats',
-              description='Format gwas summary statistics',
-              add_args_function=add_format_sumstats_args)
-def gwas_format_from_cli(args: argparse.Namespace):
-    from gsMap.format_sumstats import gwas_format
-    config = get_dataclass_from_parser(args, FormatSumstatsConfig)
-    gwas_format(config)
-
-@register_cli(name='quick_mode',
-                description='Run all the gsMap pipeline in quick mode',
-                add_args_function=add_run_all_mode_args)
-def run_all_mode_from_cli(args: argparse.Namespace):
-    from gsMap.run_all_mode import run_pipeline
-    config = get_dataclass_from_parser(args, RunAllModeConfig)
-    run_pipeline(config)
+import argparse
+import dataclasses
+import logging
+import sys
+from collections import OrderedDict, namedtuple
+from collections.abc import Callable
+from dataclasses import dataclass
+from functools import wraps
+from pathlib import Path
+from pprint import pprint
+from typing import Literal
+
+import pyfiglet
+import yaml
+
+from gsMap.__init__ import __version__
+
+# Global registry to hold functions
+cli_function_registry = OrderedDict()
+subcommand = namedtuple("subcommand", ["name", "func", "add_args_function", "description"])
+
+
+def get_gsMap_logger(logger_name):
+    logger = logging.getLogger(logger_name)
+    logger.setLevel(logging.DEBUG)
+    handler = logging.StreamHandler()
+    handler.setFormatter(
+        logging.Formatter("[{asctime}] {levelname:.5s} | {name} - {message}", style="{")
+    )
+    logger.addHandler(handler)
+    return logger
+
+
+logger = get_gsMap_logger("gsMap")
+
+
+# Decorator to register functions for cli parsing
+def register_cli(name: str, description: str, add_args_function: Callable) -> Callable:
+    def decorator(func: Callable) -> Callable:
+        def wrapper(*args, **kwargs):
+            name.replace("_", " ")
+            gsMap_main_logo = pyfiglet.figlet_format(
+                "gsMap",
+                font="doom",
+                width=80,
+                justify="center",
+            ).rstrip()
+            print(gsMap_main_logo, flush=True)
+            version_number = "Version: " + __version__
+            print(version_number.center(80), flush=True)
+            print("=" * 80, flush=True)
+            logger.info(f"Running {name}...")
+            func(*args, **kwargs)
+            logger.info(f"Finished running {name}.")
+
+        cli_function_registry[name] = subcommand(
+            name=name, func=wrapper, add_args_function=add_args_function, description=description
+        )
+        return wrapper
+
+    return decorator
+
+
+def add_shared_args(parser):
+    parser.add_argument(
+        "--workdir", type=str, required=True, help="Path to the working directory."
+    )
+    parser.add_argument("--sample_name", type=str, required=True, help="Name of the sample.")
+
+
+def add_find_latent_representations_args(parser):
+    add_shared_args(parser)
+    parser.add_argument(
+        "--input_hdf5_path", required=True, type=str, help="Path to the input HDF5 file."
+    )
+    parser.add_argument(
+        "--annotation", required=True, type=str, help="Name of the annotation in adata.obs to use."
+    )
+    parser.add_argument(
+        "--data_layer",
+        type=str,
+        default="counts",
+        required=True,
+        help='Data layer for gene expression (e.g., "count", "counts", "log1p").',
+    )
+    parser.add_argument("--epochs", type=int, default=300, help="Number of training epochs.")
+    parser.add_argument(
+        "--feat_hidden1", type=int, default=256, help="Neurons in the first hidden layer."
+    )
+    parser.add_argument(
+        "--feat_hidden2", type=int, default=128, help="Neurons in the second hidden layer."
+    )
+    parser.add_argument(
+        "--gat_hidden1", type=int, default=64, help="Units in the first GAT hidden layer."
+    )
+    parser.add_argument(
+        "--gat_hidden2", type=int, default=30, help="Units in the second GAT hidden layer."
+    )
+    parser.add_argument("--p_drop", type=float, default=0.1, help="Dropout rate.")
+    parser.add_argument("--gat_lr", type=float, default=0.001, help="Learning rate for the GAT.")
+    parser.add_argument("--n_neighbors", type=int, default=11, help="Number of neighbors for GAT.")
+    parser.add_argument(
+        "--n_comps", type=int, default=300, help="Number of principal components for PCA."
+    )
+    parser.add_argument(
+        "--weighted_adj", action="store_true", help="Use weighted adjacency in GAT."
+    )
+    parser.add_argument(
+        "--convergence_threshold", type=float, default=1e-4, help="Threshold for convergence."
+    )
+    parser.add_argument(
+        "--hierarchically",
+        action="store_true",
+        help="Enable hierarchical latent representation finding.",
+    )
+
+
+def chrom_choice(value):
+    if value.isdigit():
+        ivalue = int(value)
+        if 1 <= ivalue <= 22:
+            return ivalue
+    elif value.lower() == "all":
+        return value
+    else:
+        raise argparse.ArgumentTypeError(
+            f"'{value}' is an invalid chromosome choice. Choose from 1-22 or 'all'."
+        )
+
+
+def filter_args_for_dataclass(args_dict, data_class: dataclass):
+    return {k: v for k, v in args_dict.items() if k in data_class.__dataclass_fields__}
+
+
+def get_dataclass_from_parser(args: argparse.Namespace, data_class: dataclass):
+    remain_kwargs = filter_args_for_dataclass(vars(args), data_class)
+    print(f"Using the following arguments for {data_class.__name__}:", flush=True)
+    pprint(remain_kwargs, indent=4)
+    sys.stdout.flush()
+    return data_class(**remain_kwargs)
+
+
+def add_latent_to_gene_args(parser):
+    add_shared_args(parser)
+
+    parser.add_argument(
+        "--input_hdf5_path",
+        type=str,
+        default=None,
+        help="Path to the input HDF5 file with latent representations, if --latent_representation is specified.",
+    )
+    parser.add_argument(
+        "--no_expression_fraction", action="store_true", help="Skip expression fraction filtering."
+    )
+    parser.add_argument(
+        "--latent_representation",
+        type=str,
+        default=None,
+        help="Type of latent representation. This should exist in the h5ad obsm.",
+    )
+    parser.add_argument("--num_neighbour", type=int, default=21, help="Number of neighbors.")
+    parser.add_argument(
+        "--num_neighbour_spatial", type=int, default=101, help="Number of spatial neighbors."
+    )
+    parser.add_argument(
+        "--homolog_file",
+        type=str,
+        default=None,
+        help="Path to homologous gene conversion file (optional).",
+    )
+    parser.add_argument(
+        "--gM_slices", type=str, default=None, help="Path to the slice mean file (optional)."
+    )
+    parser.add_argument(
+        "--annotation",
+        type=str,
+        default=None,
+        help="Name of the annotation in adata.obs to use (optional).",
+    )
+
+
+def add_generate_ldscore_args(parser):
+    add_shared_args(parser)
+    parser.add_argument("--chrom", type=str, required=True, help='Chromosome id (1-22) or "all".')
+    parser.add_argument(
+        "--bfile_root",
+        type=str,
+        required=True,
+        help="Root path for genotype plink bfiles (.bim, .bed, .fam).",
+    )
+    parser.add_argument(
+        "--keep_snp_root", type=str, required=True, help="Root path for SNP files."
+    )
+    parser.add_argument(
+        "--gtf_annotation_file", type=str, required=True, help="Path to GTF annotation file."
+    )
+    parser.add_argument(
+        "--gene_window_size", type=int, default=50000, help="Gene window size in base pairs."
+    )
+    parser.add_argument(
+        "--enhancer_annotation_file", type=str, help="Path to enhancer annotation file (optional)."
+    )
+    parser.add_argument(
+        "--snp_multiple_enhancer_strategy",
+        type=str,
+        choices=["max_mkscore", "nearest_TSS"],
+        default="max_mkscore",
+        help="Strategy for handling multiple enhancers per SNP.",
+    )
+    parser.add_argument(
+        "--gene_window_enhancer_priority",
+        type=str,
+        choices=["gene_window_first", "enhancer_first", "enhancer_only"],
+        help="Priority between gene window and enhancer annotations.",
+    )
+    parser.add_argument(
+        "--spots_per_chunk", type=int, default=1000, help="Number of spots per chunk."
+    )
+    parser.add_argument("--ld_wind", type=int, default=1, help="LD window size.")
+    parser.add_argument(
+        "--ld_unit",
+        type=str,
+        choices=["SNP", "KB", "CM"],
+        default="CM",
+        help="Unit for LD window.",
+    )
+    parser.add_argument(
+        "--additional_baseline_annotation",
+        type=str,
+        default=None,
+        help="Path of additional baseline annotations",
+    )
+
+
+def add_spatial_ldsc_args(parser):
+    add_shared_args(parser)
+    parser.add_argument(
+        "--sumstats_file", type=str, required=True, help="Path to GWAS summary statistics file."
+    )
+    parser.add_argument(
+        "--w_file", type=str, required=True, help="Path to regression weight file."
+    )
+    parser.add_argument(
+        "--trait_name", type=str, required=True, help="Name of the trait being analyzed."
+    )
+    parser.add_argument(
+        "--n_blocks", type=int, default=200, help="Number of blocks for jackknife resampling."
+    )
+    parser.add_argument(
+        "--chisq_max", type=int, help="Maximum chi-square value for filtering SNPs."
+    )
+    parser.add_argument(
+        "--num_processes", type=int, default=4, help="Number of processes for parallel computing."
+    )
+    parser.add_argument(
+        "--use_additional_baseline_annotation",
+        type=bool,
+        nargs="?",
+        const=True,
+        default=True,
+        help="Use additional baseline annotations when provided",
+    )
+
+
+def add_Cauchy_combination_args(parser):
+    parser.add_argument(
+        "--workdir", type=str, required=True, help="Path to the working directory."
+    )
+    parser.add_argument("--sample_name", type=str, required=False, help="Name of the sample.")
+
+    parser.add_argument(
+        "--trait_name", type=str, required=True, help="Name of the trait being analyzed."
+    )
+    parser.add_argument(
+        "--annotation", type=str, required=True, help="Name of the annotation in adata.obs to use."
+    )
+
+    parser.add_argument(
+        "--sample_name_list",
+        type=str,
+        nargs="+",
+        required=False,
+        help="List of sample names to process. Provide as a space-separated list.",
+    )
+    parser.add_argument(
+        "--output_file",
+        type=str,
+        required=False,
+        help="Path to save the combined Cauchy results. Required when using multiple samples.",
+    )
+
+
+def add_report_args(parser):
+    add_shared_args(parser)
+    parser.add_argument(
+        "--trait_name",
+        type=str,
+        required=True,
+        help="Name of the trait to generate the report for.",
+    )
+    parser.add_argument("--annotation", type=str, required=True, help="Annotation layer name.")
+    # parser.add_argument('--plot_type', type=str, choices=['manhattan', 'GSS', 'gsMap', 'all'], default='all',
+    #                     help="Type of diagnostic plot to generate. Choose from 'manhattan', 'GSS', 'gsMap', or 'all'.")
+    parser.add_argument(
+        "--top_corr_genes", type=int, default=50, help="Number of top correlated genes to display."
+    )
+    parser.add_argument(
+        "--selected_genes",
+        type=str,
+        nargs="*",
+        help="List of specific genes to include in the report (optional).",
+    )
+    parser.add_argument(
+        "--sumstats_file", type=str, required=True, help="Path to GWAS summary statistics file."
+    )
+
+    # Optional arguments for customization
+    parser.add_argument(
+        "--fig_width", type=int, default=None, help="Width of the generated figures in pixels."
+    )
+    parser.add_argument(
+        "--fig_height", type=int, default=None, help="Height of the generated figures in pixels."
+    )
+    parser.add_argument("--point_size", type=int, default=None, help="Point size for the figures.")
+    parser.add_argument(
+        "--fig_style",
+        type=str,
+        default="light",
+        choices=["dark", "light"],
+        help="Style of the generated figures.",
+    )
+
+
+def add_create_slice_mean_args(parser):
+    parser.add_argument(
+        "--sample_name_list",
+        type=str,
+        nargs="+",
+        required=True,
+        help="List of sample names to process. Provide as a space-separated list.",
+    )
+
+    parser.add_argument(
+        "--h5ad_list",
+        type=str,
+        nargs="+",
+        help="List of h5ad file paths corresponding to the sample names. Provide as a space-separated list.",
+    )
+    parser.add_argument(
+        "--h5ad_yaml",
+        type=str,
+        default=None,
+        help="Path to the YAML file containing sample names and associated h5ad file paths",
+    )
+    parser.add_argument(
+        "--slice_mean_output_file",
+        type=str,
+        required=True,
+        help="Path to the output file for the slice mean",
+    )
+    parser.add_argument(
+        "--homolog_file", type=str, help="Path to homologous gene conversion file (optional)."
+    )
+    parser.add_argument(
+        "--data_layer",
+        type=str,
+        default="counts",
+        required=True,
+        help='Data layer for gene expression (e.g., "count", "counts", "log1p").',
+    )
+
+
+def add_format_sumstats_args(parser):
+    # Required arguments
+    parser.add_argument("--sumstats", required=True, type=str, help="Path to gwas summary data")
+    parser.add_argument(
+        "--out", required=True, type=str, help="Path to save the formatted gwas data"
+    )
+
+    # Arguments for specify column name
+    parser.add_argument(
+        "--snp",
+        default=None,
+        type=str,
+        help="Name of snp column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--a1",
+        default=None,
+        type=str,
+        help="Name of effect allele column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--a2",
+        default=None,
+        type=str,
+        help="Name of none-effect allele column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--info",
+        default=None,
+        type=str,
+        help="Name of info column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--beta",
+        default=None,
+        type=str,
+        help="Name of gwas beta column (if not a name that gsMap understands).",
+    )
+    parser.add_argument(
+        "--se",
+        default=None,
+        type=str,
+        help="Name of gwas standar error of beta column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--p",
+        default=None,
+        type=str,
+        help="Name of p-value column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--frq",
+        default=None,
+        type=str,
+        help="Name of A1 ferquency column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--n",
+        default=None,
+        type=str,
+        help="Name of sample size column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--z",
+        default=None,
+        type=str,
+        help="Name of gwas Z-statistics column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--OR",
+        default=None,
+        type=str,
+        help="Name of gwas OR column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--se_OR",
+        default=None,
+        type=str,
+        help="Name of standar error of OR column (if not a name that gsMap understands)",
+    )
+
+    # Arguments for convert SNP (chr, pos) to rsid
+    parser.add_argument(
+        "--chr",
+        default="Chr",
+        type=str,
+        help="Name of SNP chromosome column (if not a name that gsMap understands)",
+    )
+    parser.add_argument(
+        "--pos",
+        default="Pos",
+        type=str,
+        help="Name of SNP positions column (if not a name that gsMap understands)",
+    )
+    parser.add_argument("--dbsnp", default=None, type=str, help="Path to reference dnsnp file")
+    parser.add_argument(
+        "--chunksize", default=1e6, type=int, help="Chunk size for loading dbsnp file"
+    )
+
+    # Arguments for output format and quality
+    parser.add_argument(
+        "--format",
+        default="gsMap",
+        type=str,
+        help="Format of output data",
+        choices=["gsMap", "COJO"],
+    )
+    parser.add_argument("--info_min", default=0.9, type=float, help="Minimum INFO score.")
+    parser.add_argument("--maf_min", default=0.01, type=float, help="Minimum MAF.")
+    parser.add_argument(
+        "--keep_chr_pos",
+        action="store_true",
+        default=False,
+        help="Keep SNP chromosome and position columns in the output data",
+    )
+
+
+def add_run_all_mode_args(parser):
+    add_shared_args(parser)
+
+    # Required paths and configurations
+    parser.add_argument(
+        "--gsMap_resource_dir",
+        type=str,
+        required=True,
+        help="Directory containing gsMap resources (e.g., genome annotations, LD reference panel, etc.).",
+    )
+    parser.add_argument(
+        "--hdf5_path",
+        type=str,
+        required=True,
+        help="Path to the input spatial transcriptomics data (H5AD format).",
+    )
+    parser.add_argument(
+        "--annotation", type=str, required=True, help="Name of the annotation in adata.obs to use."
+    )
+    parser.add_argument(
+        "--data_layer",
+        type=str,
+        default="counts",
+        required=True,
+        help='Data layer for gene expression (e.g., "count", "counts", "log1p").',
+    )
+
+    # GWAS Data Parameters
+    parser.add_argument(
+        "--trait_name",
+        type=str,
+        help="Name of the trait for GWAS analysis (required if sumstats_file is provided).",
+    )
+    parser.add_argument(
+        "--sumstats_file",
+        type=str,
+        help="Path to GWAS summary statistics file. Either sumstats_file or sumstats_config_file is required.",
+    )
+    parser.add_argument(
+        "--sumstats_config_file",
+        type=str,
+        help="Path to GWAS summary statistics config file. Either sumstats_file or sumstats_config_file is required.",
+    )
+
+    # Homolog Data Parameters
+    parser.add_argument(
+        "--homolog_file",
+        type=str,
+        help="Path to homologous gene for converting gene names from different species to human (optional, used for cross-species analysis).",
+    )
+
+    # Maximum number of processes
+    parser.add_argument(
+        "--max_processes",
+        type=int,
+        default=10,
+        help="Maximum number of processes for parallel execution.",
+    )
+
+    parser.add_argument(
+        "--latent_representation",
+        type=str,
+        default=None,
+        help="Type of latent representation. This should exist in the h5ad obsm.",
+    )
+    parser.add_argument("--num_neighbour", type=int, default=21, help="Number of neighbors.")
+    parser.add_argument(
+        "--num_neighbour_spatial", type=int, default=101, help="Number of spatial neighbors."
+    )
+    parser.add_argument(
+        "--gM_slices", type=str, default=None, help="Path to the slice mean file (optional)."
+    )
+
+
+def ensure_path_exists(func):
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        result = func(*args, **kwargs)
+        if isinstance(result, Path):
+            if result.suffix:
+                result.parent.mkdir(parents=True, exist_ok=True, mode=0o755)
+            else:  # It's a directory path
+                result.mkdir(parents=True, exist_ok=True, mode=0o755)
+        return result
+
+    return wrapper
+
+
+@dataclass
+class ConfigWithAutoPaths:
+    workdir: str
+    sample_name: str | None
+
+    def __post_init__(self):
+        if self.workdir is None:
+            raise ValueError("workdir must be provided.")
+
+    @property
+    @ensure_path_exists
+    def hdf5_with_latent_path(self) -> Path:
+        return Path(
+            f"{self.workdir}/{self.sample_name}/find_latent_representations/{self.sample_name}_add_latent.h5ad"
+        )
+
+    @property
+    @ensure_path_exists
+    def mkscore_feather_path(self) -> Path:
+        return Path(
+            f"{self.workdir}/{self.sample_name}/latent_to_gene/{self.sample_name}_gene_marker_score.feather"
+        )
+
+    @property
+    @ensure_path_exists
+    def ldscore_save_dir(self) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/generate_ldscore")
+
+    @property
+    @ensure_path_exists
+    def ldsc_save_dir(self) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/spatial_ldsc")
+
+    @property
+    @ensure_path_exists
+    def cauchy_save_dir(self) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/cauchy_combination")
+
+    @ensure_path_exists
+    def get_report_dir(self, trait_name: str) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/report/{trait_name}")
+
+    def get_gsMap_report_file(self, trait_name: str) -> Path:
+        return (
+            self.get_report_dir(trait_name) / f"{self.sample_name}_{trait_name}_gsMap_Report.html"
+        )
+
+    @ensure_path_exists
+    def get_manhattan_html_plot_path(self, trait_name: str) -> Path:
+        return Path(
+            f"{self.workdir}/{self.sample_name}/report/{trait_name}/manhattan_plot/{self.sample_name}_{trait_name}_Diagnostic_Manhattan_Plot.html"
+        )
+
+    @ensure_path_exists
+    def get_GSS_plot_dir(self, trait_name: str) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/report/{trait_name}/GSS_plot")
+
+    def get_GSS_plot_select_gene_file(self, trait_name: str) -> Path:
+        return self.get_GSS_plot_dir(trait_name) / "plot_genes.csv"
+
+    @ensure_path_exists
+    def get_ldsc_result_file(self, trait_name: str) -> Path:
+        return Path(f"{self.ldsc_save_dir}/{self.sample_name}_{trait_name}.csv.gz")
+
+    @ensure_path_exists
+    def get_cauchy_result_file(self, trait_name: str) -> Path:
+        return Path(f"{self.cauchy_save_dir}/{self.sample_name}_{trait_name}.Cauchy.csv.gz")
+
+    @ensure_path_exists
+    def get_gene_diagnostic_info_save_path(self, trait_name: str) -> Path:
+        return Path(
+            f"{self.workdir}/{self.sample_name}/report/{trait_name}/{self.sample_name}_{trait_name}_Gene_Diagnostic_Info.csv"
+        )
+
+    @ensure_path_exists
+    def get_gsMap_plot_save_dir(self, trait_name: str) -> Path:
+        return Path(f"{self.workdir}/{self.sample_name}/report/{trait_name}/gsMap_plot")
+
+    def get_gsMap_html_plot_save_path(self, trait_name: str) -> Path:
+        return (
+            self.get_gsMap_plot_save_dir(trait_name)
+            / f"{self.sample_name}_{trait_name}_gsMap_plot.html"
+        )
+
+
+@dataclass
+class CreateSliceMeanConfig:
+    slice_mean_output_file: str | Path
+    h5ad_yaml: str | dict | None = None
+    sample_name_list: list | None = None
+    h5ad_list: list | None = None
+    homolog_file: str | None = None
+    species: str | None = None
+    data_layer: str = None
+
+    def __post_init__(self):
+        if self.h5ad_list is None and self.h5ad_yaml is None:
+            raise ValueError("At least one of --h5ad_list or --h5ad_yaml must be provided.")
+        if self.h5ad_yaml is not None:
+            if isinstance(self.h5ad_yaml, str):
+                logger.info(f"Reading h5ad yaml file: {self.h5ad_yaml}")
+            h5ad_dict = (
+                yaml.safe_load(open(self.h5ad_yaml))
+                if isinstance(self.h5ad_yaml, str)
+                else self.h5ad_yaml
+            )
+        elif self.sample_name_list and self.h5ad_list:
+            logger.info("Reading sample name list and h5ad list")
+            h5ad_dict = dict(zip(self.sample_name_list, self.h5ad_list, strict=False))
+        else:
+            raise ValueError(
+                "Please provide either h5ad_yaml or both sample_name_list and h5ad_list."
+            )
+
+        # check if sample names is unique
+        assert len(h5ad_dict) == len(set(h5ad_dict)), "Sample names must be unique."
+        assert len(h5ad_dict) > 1, "At least two samples are required."
+
+        logger.info(f"Input h5ad files: {h5ad_dict}")
+
+        # Check if all files exist
+        self.h5ad_dict = {}
+        for sample_name, h5ad_file in h5ad_dict.items():
+            h5ad_file = Path(h5ad_file)
+            if not h5ad_file.exists():
+                raise FileNotFoundError(f"{h5ad_file} does not exist.")
+            self.h5ad_dict[sample_name] = h5ad_file
+
+        self.slice_mean_output_file = Path(self.slice_mean_output_file)
+        self.slice_mean_output_file.parent.mkdir(parents=True, exist_ok=True)
+
+        verify_homolog_file_format(self)
+
+
+@dataclass
+class FindLatentRepresentationsConfig(ConfigWithAutoPaths):
+    input_hdf5_path: str
+    # output_hdf5_path: str
+    annotation: str = None
+    data_layer: str = None
+
+    epochs: int = 300
+    feat_hidden1: int = 256
+    feat_hidden2: int = 128
+    feat_cell: int = 3000
+    gat_hidden1: int = 64
+    gat_hidden2: int = 30
+    p_drop: float = 0.1
+    gat_lr: float = 0.001
+    gcn_decay: float = 0.01
+    n_neighbors: int = 11
+    label_w: float = 1
+    rec_w: float = 1
+    input_pca: bool = True
+    n_comps: int = 300
+    weighted_adj: bool = False
+    nheads: int = 3
+    var: bool = False
+    convergence_threshold: float = 1e-4
+    hierarchically: bool = False
+
+    def __post_init__(self):
+        # self.output_hdf5_path = self.hdf5_with_latent_path
+        if self.hierarchically:
+            if self.annotation is None:
+                raise ValueError("annotation must be provided if hierarchically is True.")
+            logger.info(
+                "------Hierarchical mode is enabled. This will find the latent representations within each annotation."
+            )
+
+        # remind for not providing annotation
+        if self.annotation is None:
+            logger.warning(
+                "annotation is not provided. This will find the latent representations for the whole dataset."
+            )
+        else:
+            logger.info(f"------Find latent representations for {self.annotation}...")
+
+
+@dataclass
+class LatentToGeneConfig(ConfigWithAutoPaths):
+    # input_hdf5_with_latent_path: str
+    # output_feather_path: str
+    input_hdf5_path: str | Path = None
+    no_expression_fraction: bool = False
+    latent_representation: str = None
+    num_neighbour: int = 21
+    num_neighbour_spatial: int = 101
+    homolog_file: str = None
+    gM_slices: str = None
+    annotation: str = None
+    species: str = None
+
+    def __post_init__(self):
+        if self.input_hdf5_path is None:
+            self.input_hdf5_path = self.hdf5_with_latent_path
+            assert self.input_hdf5_path.exists(), (
+                f"{self.input_hdf5_path} does not exist. Please run FindLatentRepresentations first."
+            )
+        else:
+            assert Path(self.input_hdf5_path).exists(), f"{self.input_hdf5_path} does not exist."
+            # copy to self.hdf5_with_latent_path
+            import shutil
+
+            shutil.copy2(self.input_hdf5_path, self.hdf5_with_latent_path)
+
+        if self.latent_representation is not None:
+            logger.info(f"Using the provided latent representation: {self.latent_representation}")
+        else:
+            self.latent_representation = "latent_GVAE"
+            logger.info(f"Using default latent representation: {self.latent_representation}")
+
+        if self.gM_slices is not None:
+            assert Path(self.gM_slices).exists(), f"{self.gM_slices} does not exist."
+            logger.info(f"Using the provided slice mean file: {self.gM_slices}.")
+
+        verify_homolog_file_format(self)
+
+
+def verify_homolog_file_format(config):
+    if config.homolog_file is not None:
+        logger.info(
+            f"User provided homolog file to map gene names to human: {config.homolog_file}"
+        )
+        # check the format of the homolog file
+        with open(config.homolog_file) as f:
+            first_line = f.readline().strip()
+            _n_col = len(first_line.split())
+            if _n_col != 2:
+                raise ValueError(
+                    f"Invalid homolog file format. Expected 2 columns, first column should be other species gene name, second column should be human gene name. "
+                    f"Got {_n_col} columns in the first line."
+                )
+            else:
+                first_col_name, second_col_name = first_line.split()
+                config.species = first_col_name
+                logger.info(
+                    f"Homolog file provided and will map gene name from column1:{first_col_name} to column2:{second_col_name}"
+                )
+    else:
+        logger.info("No homolog file provided. Run in human mode.")
+
+
+@dataclass
+class GenerateLDScoreConfig(ConfigWithAutoPaths):
+    chrom: int | str
+
+    bfile_root: str
+    keep_snp_root: str | None
+
+    # annotation by gene distance
+    gtf_annotation_file: str
+    gene_window_size: int = 50000
+
+    # annotation by enhancer
+    enhancer_annotation_file: str = None
+    snp_multiple_enhancer_strategy: Literal["max_mkscore", "nearest_TSS"] = "max_mkscore"
+    gene_window_enhancer_priority: (
+        Literal["gene_window_first", "enhancer_first", "enhancer_only"] | None
+    ) = None
+
+    # for calculating ld score
+    additional_baseline_annotation: str = None
+    spots_per_chunk: int = 1_000
+    ld_wind: int = 1
+    ld_unit: str = "CM"
+
+    # zarr config
+    ldscore_save_format: Literal["feather", "zarr", "quick_mode"] = "feather"
+
+    zarr_chunk_size: tuple[int, int] = None
+
+    # for pre calculating the SNP Gene ldscore Weight
+    save_pre_calculate_snp_gene_weight_matrix: bool = False
+
+    baseline_annotation_dir: str | None = None
+    SNP_gene_pair_dir: str | None = None
+
+    def __post_init__(self):
+        # if self.mkscore_feather_file is None:
+        #     self.mkscore_feather_file = self._get_mkscore_feather_path()
+
+        if (
+            self.enhancer_annotation_file is not None
+            and self.gene_window_enhancer_priority is None
+        ):
+            logger.warning(
+                "enhancer_annotation_file is provided but gene_window_enhancer_priority is not provided. "
+                "by default, gene_window_enhancer_priority is set to 'enhancer_only', when enhancer_annotation_file is provided."
+            )
+            self.gene_window_enhancer_priority = "enhancer_only"
+        if (
+            self.enhancer_annotation_file is None
+            and self.gene_window_enhancer_priority is not None
+        ):
+            logger.warning(
+                "gene_window_enhancer_priority is provided but enhancer_annotation_file is not provided. "
+                "by default, gene_window_enhancer_priority is set to None, when enhancer_annotation_file is not provided."
+            )
+            self.gene_window_enhancer_priority = None
+        assert self.gene_window_enhancer_priority in [
+            None,
+            "gene_window_first",
+            "enhancer_first",
+            "enhancer_only",
+        ], (
+            f"gene_window_enhancer_priority must be one of None, 'gene_window_first', 'enhancer_first', 'enhancer_only', but got {self.gene_window_enhancer_priority}."
+        )
+        if self.gene_window_enhancer_priority in ["gene_window_first", "enhancer_first"]:
+            logger.info(
+                "Both gene_window and enhancer annotation will be used to calculate LD score. "
+            )
+            logger.info(
+                f"SNP within +-{self.gene_window_size} bp of gene body will be used and enhancer annotation will be used to calculate LD score. If a snp maps to multiple enhancers, the strategy to choose by your select strategy: {self.snp_multiple_enhancer_strategy}."
+            )
+        elif self.gene_window_enhancer_priority == "enhancer_only":
+            logger.info("Only enhancer annotation will be used to calculate LD score. ")
+        else:
+            logger.info(
+                f"Only gene window annotation will be used to calculate LD score. SNP within +-{self.gene_window_size} bp of gene body will be used. "
+            )
+
+        # remind for baseline annotation
+        if self.additional_baseline_annotation is None:
+            logger.info(
+                "------Baseline annotation is not provided. Default baseline annotation will be used."
+            )
+        else:
+            logger.info(
+                "------Baseline annotation is provided. Additional baseline annotation will be used with the default baseline annotation."
+            )
+            logger.info(
+                f"------Baseline annotation directory: {self.additional_baseline_annotation}"
+            )
+            # check the existence of baseline annotation
+            if self.chrom == "all":
+                for chrom in range(1, 23):
+                    chrom = str(chrom)
+                    baseline_annotation_path = (
+                        Path(self.additional_baseline_annotation) / f"baseline.{chrom}.annot.gz"
+                    )
+                    if not baseline_annotation_path.exists():
+                        raise FileNotFoundError(
+                            f"baseline.{chrom}.annot.gz is not found in {self.additional_baseline_annotation}."
+                        )
+            else:
+                baseline_annotation_path = (
+                    Path(self.additional_baseline_annotation) / f"baseline.{self.chrom}.annot.gz"
+                )
+                if not baseline_annotation_path.exists():
+                    raise FileNotFoundError(
+                        f"baseline.{self.chrom}.annot.gz is not found in {self.additional_baseline_annotation}."
+                    )
+
+        # set the default zarr chunk size
+        if self.ldscore_save_format == "zarr" and self.zarr_chunk_size is None:
+            self.zarr_chunk_size = (10_000, self.spots_per_chunk)
+
+
+@dataclass
+class SpatialLDSCConfig(ConfigWithAutoPaths):
+    w_file: str
+    # ldscore_save_dir: str
+    use_additional_baseline_annotation: bool = True
+    trait_name: str | None = None
+    sumstats_file: str | None = None
+    sumstats_config_file: str | None = None
+    num_processes: int = 4
+    not_M_5_50: bool = False
+    n_blocks: int = 200
+    chisq_max: int | None = None
+    all_chunk: int | None = None
+    chunk_range: tuple[int, int] | None = None
+
+    ldscore_save_format: Literal["feather", "zarr", "quick_mode"] = "feather"
+
+    spots_per_chunk_quick_mode: int = 1_000
+    snp_gene_weight_adata_path: str | None = None
+
+    def __post_init__(self):
+        super().__post_init__()
+        if self.sumstats_file is None and self.sumstats_config_file is None:
+            raise ValueError("One of sumstats_file and sumstats_config_file must be provided.")
+        if self.sumstats_file is not None and self.sumstats_config_file is not None:
+            raise ValueError(
+                "Only one of sumstats_file and sumstats_config_file must be provided."
+            )
+        if self.sumstats_file is not None and self.trait_name is None:
+            raise ValueError("trait_name must be provided if sumstats_file is provided.")
+        if self.sumstats_config_file is not None and self.trait_name is not None:
+            raise ValueError(
+                "trait_name must not be provided if sumstats_config_file is provided."
+            )
+        self.sumstats_config_dict = {}
+        # load the sumstats config file
+        if self.sumstats_config_file is not None:
+            import yaml
+
+            with open(self.sumstats_config_file) as f:
+                config = yaml.load(f, Loader=yaml.FullLoader)
+            for _trait_name, sumstats_file in config.items():
+                assert Path(sumstats_file).exists(), f"{sumstats_file} does not exist."
+        # load the sumstats file
+        elif self.sumstats_file is not None:
+            self.sumstats_config_dict[self.trait_name] = self.sumstats_file
+        else:
+            raise ValueError("One of sumstats_file and sumstats_config_file must be provided.")
+
+        for sumstats_file in self.sumstats_config_dict.values():
+            assert Path(sumstats_file).exists(), f"{sumstats_file} does not exist."
+
+        # check if additional baseline annotation is exist
+        # self.use_additional_baseline_annotation = False
+
+        if self.use_additional_baseline_annotation:
+            self.process_additional_baseline_annotation()
+
+    def process_additional_baseline_annotation(self):
+        additional_baseline_annotation = Path(self.ldscore_save_dir) / "additional_baseline"
+        dir_exists = additional_baseline_annotation.exists()
+
+        if not dir_exists:
+            self.use_additional_baseline_annotation = False
+            # if self.use_additional_baseline_annotation:
+            #     logger.warning(f"additional_baseline directory is not found in {self.ldscore_save_dir}.")
+            #     print('''\
+            #         if you want to use additional baseline annotation,
+            #         please provide additional baseline annotation when calculating ld score.
+            #         ''')
+            #     raise FileNotFoundError(
+            #         f'additional_baseline directory is not found.')
+            # return
+            # self.use_additional_baseline_annotation = self.use_additional_baseline_annotation or True
+        else:
+            logger.info(
+                "------Additional baseline annotation is provided. It will be used with the default baseline annotation."
+            )
+            logger.info(
+                f"------Additional baseline annotation directory: {additional_baseline_annotation}"
+            )
+
+            chrom_list = range(1, 23)
+            for chrom in chrom_list:
+                baseline_annotation_path = (
+                    additional_baseline_annotation / f"baseline.{chrom}.l2.ldscore.feather"
+                )
+                if not baseline_annotation_path.exists():
+                    raise FileNotFoundError(
+                        f"baseline.{chrom}.annot.gz is not found in {additional_baseline_annotation}."
+                    )
+        return None
+
+
+@dataclass
+class CauchyCombinationConfig(ConfigWithAutoPaths):
+    trait_name: str
+    annotation: str
+    sample_name_list: list[str] = dataclasses.field(default_factory=list)
+    output_file: str | Path | None = None
+
+    def __post_init__(self):
+        if self.sample_name is not None:
+            if len(self.sample_name_list) > 0:
+                raise ValueError("Only one of sample_name and sample_name_list must be provided.")
+            else:
+                self.sample_name_list = [self.sample_name]
+                self.output_file = (
+                    self.get_cauchy_result_file(self.trait_name)
+                    if self.output_file is None
+                    else self.output_file
+                )
+        else:
+            assert len(self.sample_name_list) > 0, "At least one sample name must be provided."
+            assert self.output_file is not None, (
+                "Output_file must be provided if sample_name_list is provided."
+            )
+
+
+@dataclass
+class VisualizeConfig(ConfigWithAutoPaths):
+    trait_name: str
+
+    annotation: str = None
+    fig_title: str = None
+    fig_height: int = 600
+    fig_width: int = 800
+    point_size: int = None
+    fig_style: Literal["dark", "light"] = "light"
+
+
+@dataclass
+class DiagnosisConfig(ConfigWithAutoPaths):
+    annotation: str
+    # mkscore_feather_file: str
+
+    trait_name: str
+    sumstats_file: str
+    plot_type: Literal["manhattan", "GSS", "gsMap", "all"] = "all"
+    top_corr_genes: int = 50
+    selected_genes: list[str] | None = None
+
+    fig_width: int | None = None
+    fig_height: int | None = None
+    point_size: int | None = None
+    fig_style: Literal["dark", "light"] = "light"
+
+    def __post_init__(self):
+        if any([self.fig_width, self.fig_height, self.point_size]):
+            logger.info("Customizing the figure size and point size.")
+            assert all([self.fig_width, self.fig_height, self.point_size]), (
+                "All of fig_width, fig_height, and point_size must be provided."
+            )
+            self.customize_fig = True
+        else:
+            self.customize_fig = False
+
+
+@dataclass
+class ReportConfig(DiagnosisConfig):
+    pass
+
+
+@dataclass
+class RunAllModeConfig(ConfigWithAutoPaths):
+    gsMap_resource_dir: str
+
+    # == ST DATA PARAMETERS ==
+    hdf5_path: str
+    annotation: str
+    data_layer: str = "X"
+
+    # == latent 2 Gene PARAMETERS ==
+    gM_slices: str | None = None
+    latent_representation: str = None
+    num_neighbour: int = 21
+    num_neighbour_spatial: int = 101
+
+    # ==GWAS DATA PARAMETERS==
+    trait_name: str | None = None
+    sumstats_file: str | None = None
+    sumstats_config_file: str | None = None
+
+    # === homolog PARAMETERS ===
+    homolog_file: str | None = None
+
+    max_processes: int = 10
+
+    def __post_init__(self):
+        super().__post_init__()
+        self.gtffile = (
+            f"{self.gsMap_resource_dir}/genome_annotation/gtf/gencode.v39lift37.annotation.gtf"
+        )
+        self.bfile_root = (
+            f"{self.gsMap_resource_dir}/LD_Reference_Panel/1000G_EUR_Phase3_plink/1000G.EUR.QC"
+        )
+        self.keep_snp_root = f"{self.gsMap_resource_dir}/LDSC_resource/hapmap3_snps/hm"
+        self.w_file = f"{self.gsMap_resource_dir}/LDSC_resource/weights_hm3_no_hla/weights."
+        self.snp_gene_weight_adata_path = (
+            f"{self.gsMap_resource_dir}/quick_mode/snp_gene_weight_matrix.h5ad"
+        )
+        self.baseline_annotation_dir = Path(
+            f"{self.gsMap_resource_dir}/quick_mode/baseline"
+        ).resolve()
+        self.SNP_gene_pair_dir = Path(
+            f"{self.gsMap_resource_dir}/quick_mode/SNP_gene_pair"
+        ).resolve()
+        # check the existence of the input files and resources files
+        for file in [self.hdf5_path, self.gtffile]:
+            if not Path(file).exists():
+                raise FileNotFoundError(f"File {file} does not exist.")
+
+        if self.sumstats_file is None and self.sumstats_config_file is None:
+            raise ValueError("One of sumstats_file and sumstats_config_file must be provided.")
+        if self.sumstats_file is not None and self.sumstats_config_file is not None:
+            raise ValueError(
+                "Only one of sumstats_file and sumstats_config_file must be provided."
+            )
+        if self.sumstats_file is not None and self.trait_name is None:
+            raise ValueError("trait_name must be provided if sumstats_file is provided.")
+        if self.sumstats_config_file is not None and self.trait_name is not None:
+            raise ValueError(
+                "trait_name must not be provided if sumstats_config_file is provided."
+            )
+        self.sumstats_config_dict = {}
+        # load the sumstats config file
+        if self.sumstats_config_file is not None:
+            import yaml
+
+            with open(self.sumstats_config_file) as f:
+                config = yaml.load(f, Loader=yaml.FullLoader)
+            for trait_name, sumstats_file in config.items():
+                assert Path(sumstats_file).exists(), f"{sumstats_file} does not exist."
+                self.sumstats_config_dict[trait_name] = sumstats_file
+        # load the sumstats file
+        elif self.sumstats_file is not None and self.trait_name is not None:
+            self.sumstats_config_dict[self.trait_name] = self.sumstats_file
+        else:
+            raise ValueError("One of sumstats_file and sumstats_config_file must be provided.")
+
+        for sumstats_file in self.sumstats_config_dict.values():
+            assert Path(sumstats_file).exists(), f"{sumstats_file} does not exist."
+
+
+@dataclass
+class FormatSumstatsConfig:
+    sumstats: str
+    out: str
+    dbsnp: str
+    snp: str = None
+    a1: str = None
+    a2: str = None
+    info: str = None
+    beta: str = None
+    se: str = None
+    p: str = None
+    frq: str = None
+    n: str = None
+    z: str = None
+    OR: str = None
+    se_OR: str = None
+    format: str = None
+    chr: str = None
+    pos: str = None
+    chunksize: int = 1e7
+    info_min: float = 0.9
+    maf_min: float = 0.01
+    keep_chr_pos: bool = False
+
+
+@register_cli(
+    name="run_find_latent_representations",
+    description="Run Find_latent_representations \nFind the latent representations of each spot by running GNN-VAE",
+    add_args_function=add_find_latent_representations_args,
+)
+def run_find_latent_representation_from_cli(args: argparse.Namespace):
+    from gsMap.find_latent_representation import run_find_latent_representation
+
+    config = get_dataclass_from_parser(args, FindLatentRepresentationsConfig)
+    run_find_latent_representation(config)
+
+
+@register_cli(
+    name="run_latent_to_gene",
+    description="Run Latent_to_gene \nEstimate gene marker gene scores for each spot by using latent representations from nearby spots",
+    add_args_function=add_latent_to_gene_args,
+)
+def run_latent_to_gene_from_cli(args: argparse.Namespace):
+    from gsMap.latent_to_gene import run_latent_to_gene
+
+    config = get_dataclass_from_parser(args, LatentToGeneConfig)
+    run_latent_to_gene(config)
+
+
+@register_cli(
+    name="run_generate_ldscore",
+    description="Run Generate_ldscore \nGenerate LD scores for each spot",
+    add_args_function=add_generate_ldscore_args,
+)
+def run_generate_ldscore_from_cli(args: argparse.Namespace):
+    from gsMap.generate_ldscore import run_generate_ldscore
+
+    config = get_dataclass_from_parser(args, GenerateLDScoreConfig)
+    run_generate_ldscore(config)
+
+
+@register_cli(
+    name="run_spatial_ldsc",
+    description="Run Spatial_ldsc \nRun spatial LDSC for each spot",
+    add_args_function=add_spatial_ldsc_args,
+)
+def run_spatial_ldsc_from_cli(args: argparse.Namespace):
+    from gsMap.spatial_ldsc_multiple_sumstats import run_spatial_ldsc
+
+    config = get_dataclass_from_parser(args, SpatialLDSCConfig)
+    run_spatial_ldsc(config)
+
+
+@register_cli(
+    name="run_cauchy_combination",
+    description="Run Cauchy_combination for each annotation",
+    add_args_function=add_Cauchy_combination_args,
+)
+def run_Cauchy_combination_from_cli(args: argparse.Namespace):
+    from gsMap.cauchy_combination_test import run_Cauchy_combination
+
+    config = get_dataclass_from_parser(args, CauchyCombinationConfig)
+    run_Cauchy_combination(config)
+
+
+@register_cli(
+    name="run_report",
+    description="Run Report to generate diagnostic plots and tables",
+    add_args_function=add_report_args,
+)
+def run_Report_from_cli(args: argparse.Namespace):
+    from gsMap.report import run_report
+
+    config = get_dataclass_from_parser(args, ReportConfig)
+    run_report(config)
+
+
+@register_cli(
+    name="format_sumstats",
+    description="Format gwas summary statistics",
+    add_args_function=add_format_sumstats_args,
+)
+def gwas_format_from_cli(args: argparse.Namespace):
+    from gsMap.format_sumstats import gwas_format
+
+    config = get_dataclass_from_parser(args, FormatSumstatsConfig)
+    gwas_format(config)
+
+
+@register_cli(
+    name="quick_mode",
+    description="Run all the gsMap pipeline in quick mode",
+    add_args_function=add_run_all_mode_args,
+)
+def run_all_mode_from_cli(args: argparse.Namespace):
+    from gsMap.run_all_mode import run_pipeline
+
+    config = get_dataclass_from_parser(args, RunAllModeConfig)
+    run_pipeline(config)
+
+
+@register_cli(
+    name="create_slice_mean",
+    description="Create slice mean from multiple h5ad files",
+    add_args_function=add_create_slice_mean_args,
+)
+def create_slice_mean_from_cli(args: argparse.Namespace):
+    from gsMap.create_slice_mean import run_create_slice_mean
+
+    config = get_dataclass_from_parser(args, CreateSliceMeanConfig)
+    run_create_slice_mean(config)