gsMap 1.62__py3-none-any.whl → 1.64__py3-none-any.whl

gsMap/config.py

@@ -1,36 +1,42 @@
 import argparse
 import logging
-from dataclasses import dataclass, field
-from pprint import pprint
-from typing import Union, Literal
-from pathlib import Path
-
 from collections import OrderedDict, namedtuple
+from dataclasses import dataclass
+from pathlib import Path
+from pprint import pprint
 from typing import Callable
-from gsMap.__init__ import __version__
+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'])
-logger = logging.getLogger(__name__)
-logger.setLevel(logging.DEBUG)
-handler = logging.StreamHandler()
-handler.setFormatter(logging.Formatter(
-    '[{asctime}] {levelname:6s} {message}', style='{'))
-logger.addHandler(handler)
 
 
+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, )
+            print(gsMap_main_logo, flush=True)
             version_number = 'Version: ' + __version__
-            print(version_number.center(80))
-            print('=' * 80)
+            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}.")
@@ -41,50 +47,28 @@ def register_cli(name: str, description: str, add_args_function: Callable) -> Ca
 
     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):
-    parser.add_argument('--input_hdf5_path', required=True, type=str, help='Path to the input hdf5 file.')
-    parser.add_argument('--output_hdf5_path', required=True, type=str, help='Path to the output hdf5 file.')
-    parser.add_argument('--sample_name', required=True, type=str, help='Name of the sample.')
-    parser.add_argument('--annotation', default=None, type=str, help='Name of the annotation layer.')
-    parser.add_argument('--type', default=None, type=str, help="The gene expression layer of the input data (e.g., 'count', 'counts', 'log1p').")
-    parser.add_argument('--epochs', default=300, type=int,
-                        help="Number of training epochs for the GNN-VAE model. Default is 300.")
-
-    parser.add_argument('--feat_hidden1', default=256, type=int,
-                        help="Number of neurons in the first hidden layer of the feature extraction network. Default is 256.")
-    parser.add_argument('--feat_hidden2', default=128, type=int,
-                        help="Number of neurons in the second hidden layer of the feature extraction network. Default is 128.")
-    parser.add_argument('--feat_cell', default=3000, type=int,
-                        help="Number of top variable genes to select. Default is 3000.")
-    parser.add_argument('--gcn_hidden1', default=64, type=int,
-                        help="Number of units in the first hidden layer of the GCN. Default is 64.")
-    parser.add_argument('--gcn_hidden2', default=30, type=int,
-                        help="Number of units in the second hidden layer of the GCN. Default is 30.")
-    parser.add_argument('--p_drop', default=0.1, type=float,
-                        help="Dropout rate used in the GNN-VAE model. Default is 0.1.")
-    parser.add_argument('--gcn_lr', default=0.001, type=float,
-                        help="Learning rate for the GCN network. Default is 0.001.")
-    parser.add_argument('--gcn_decay', default=0.01, type=float,
-                        help="Weight decay (L2 penalty) for the GCN network. Default is 0.01.")
-    parser.add_argument('--n_neighbors', default=11, type=int,
-                        help="Number of neighbors to consider for graph construction in GCN. Default is 11.")
-    parser.add_argument('--label_w', default=1, type=float,
-                        help="Weight of the label loss in the loss function. Default is 1.")
-    parser.add_argument('--rec_w', default=1, type=float,
-                        help="Weight of the reconstruction loss in the loss function. Default is 1.")
-    parser.add_argument('--n_comps', default=300, type=int,
-                        help="Number of principal components to keep if PCA is performed. Default is 300.")
-    parser.add_argument('--weighted_adj', action='store_true',
-                        help="Use a weighted adjacency matrix in GCN. Default is False.")
-    parser.add_argument('--nheads', default=3, type=int,
-                        help="Number of heads in the attention mechanism of the GNN. Default is 3.")
-    parser.add_argument('--var', action='store_true',
-                        help="Enable var. Use --var to enable. Default is False.")
-    parser.add_argument('--convergence_threshold', default=1e-4, type=float,
-                        help="Threshold for convergence during training. Training stops if the loss change is below this threshold. Default is 1e-4.")
-    parser.add_argument('--hierarchically', action='store_true',
-                        help="Find latent representations hierarchically. Use --hierarchically to enable. Default is False.")
+    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', required=True, type=str, help='Data layer for gene expression (e.g., "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('--var', action='store_true', help='Enable variance calculations.')
+    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):
@@ -109,297 +93,284 @@ def get_dataclass_from_parser(args: argparse.Namespace, data_class: dataclass):
     return data_class(**remain_kwargs)
 
 
-def add_generate_ldscore_args(parser):
-    parser.add_argument('--sample_name', type=str, required=True, help='Sample name')
-    parser.add_argument('--chrom', type=str, required=True, help='Chromosome number (1-22) or "all"')
-    parser.add_argument('--ldscore_save_dir', type=str, required=True, help='Directory to save ld score files')
-    parser.add_argument('--mkscore_feather_file', type=str, required=True, help='Mkscore feather file path')
-
-    # additional baseline annotation
-    parser.add_argument('--additional_baseline_annotation_dir_path', type=str, default=None,)
-
-    # reference panel
-    parser.add_argument('--bfile_root', type=str, required=True, help='Bfile root path')
-    parser.add_argument('--keep_snp_root', type=str, required=True, help='Keep SNP root path')
-
-    # Annotation by gene distance
-    parser.add_argument('--gtf_annotation_file', type=str, required=True, help='GTF file path')
-    parser.add_argument('--gene_window_size', type=int, default=50000, help='Gene window size')
-
-    # Enhancer annotation
-    parser.add_argument('--enhancer_annotation_file', type=str, default=None,
-                        help='Enhancer annotation bed file path, optional.')
-    parser.add_argument('--snp_multiple_enhancer_strategy', type=str, default='max_mkscore',
-                        choices=['max_mkscore', 'nearest_TSS'], help='Strategy for multiple enhancers per SNP')
-    parser.add_argument('--gene_window_enhancer_priority', type=str, default=None,
-                        choices=['gene_window_first', 'enhancer_first', 'enhancer_only'],
-                        help='Priority between gene window and enhancer')
-
-    # Arguments for calculating ld score
-    parser.add_argument('--spots_per_chunk', type=int, default=5_000, 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, default='CM', help='LD window unit (SNP/KB/CM)',
-                        choices=['SNP', 'KB', 'CM'])
-
-
 def add_latent_to_gene_args(parser):
-    parser.add_argument('--input_hdf5_with_latent_path', type=str, required=True,
-                        help='Path to the input HDF5 file which contains latent representations.')
-    parser.add_argument('--sample_name', type=str, required=True, help='Name of the sample.')
-    parser.add_argument('--output_feather_path', type=str, required=True,
-                        help='Path to save output gene marker score feather file.')
-    parser.add_argument('--annotation', default=None, type=str, help='Name of the annotation layer.')
-    parser.add_argument('--type', default=None, type=str, help="Type of input data (e.g., 'count', 'counts').")
-
-    # no_expression_fraction
-    parser.add_argument('--no_expression_fraction', action='store_true', default=False,
-                        help='Flag to not use expression fraction as filter when calculate the maker score. Default is False.')
-
-    parser.add_argument('--latent_representation', type=str, default='latent_GVAE',
-                        choices=['latent_GVAE', 'latent_PCA'],
-                        help='Type of latent representation. Default is "latent_GVAE".')
-    parser.add_argument('--num_neighbour', type=int, default=21,
-                        help='Number of neighbours to consider. Default is 21.')
-    parser.add_argument('--num_neighbour_spatial', type=int, default=101,
-                        help='Number of spatial neighbours to consider. Default is 101.')
-    parser.add_argument('--species', type=str, default=None, help='Species name, which is the column name in the homolog gene conversion file.')
-    parser.add_argument('--gs_species', type=str, default=None, help='Homologous gene conversion file path, if applicable.')
-    parser.add_argument('--gM_slices', type=str, default=None, help='The mean Gene marker scores path across multiple slices.')
+    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_spatial_ldsc_args(parser):
-    # Group for GWAS input data
-    parser.add_argument('--sample_name', required=True, help="Name of the spatial transcriptomic dataset.")
+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')
 
-    parser.add_argument('--sumstats_file', default=None, help="Path to GWAS summary statistics file.")
-    parser.add_argument('--sumstats_config_file', default=None, help="Path to GWAS summary statistics config file.")
-    parser.add_argument('--w_file', required=True, help="Path to regression weight file.")
-    parser.add_argument('--ldscore_input_dir', required=True, help="Input directory for LD Score files.")
-    parser.add_argument('--ldsc_save_dir', required=True, help="Directory to save Spatial LDSC results.")
-    parser.add_argument('--trait_name', default=None, help="Name of the trait.")
-    parser.add_argument('--not_M_5_50', action='store_true', help="Flag to not use M 5 50 in calculations.")
-    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('--all_chunk', type=int, help="Number of chunks for processing spatial data.")
 
-    # if use additional baseline annotation
-    parser.add_argument('--disable_additional_baseline_annotation', action='store_true', default=False,)
+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).')
 
-    parser.add_argument('--num_processes', type=int, default=4, help="Number of processes for parallel computing.")
 
-    return parser
+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):
-    # Required arguments
-    parser.add_argument('--input_hdf5_path', required=True, type=str, help='Path to the HDF5 file')
-    parser.add_argument('--input_ldsc_dir', required=True, type=str, help='Directory containing LDSC results')
-    parser.add_argument('--output_cauchy_dir', required=True, type=str,
-                        help='Output directory for Cauchy combination results')
-    parser.add_argument('--sample_name', required=True, type=str, help='Name of the sample')
-    parser.add_argument('--trait_name', required=True, type=str, help='Name of the trait')
-    parser.add_argument('--annotation', required=True, type=str, help='Annotation layer name')
-
-    # Optional arguments
-    parser.add_argument('--meta', default=None, type=str, )
-    parser.add_argument('--slide', default=None, type=str, )
-
-
-
-def add_Visualization_args(parser):
-    # Required arguments
-    parser.add_argument('--input_hdf5_path', required=True, type=str, help='Path to the HDF5 file')
-    parser.add_argument('--input_ldsc_dir', required=True, type=str, help='Directory containing LDSC results')
-    parser.add_argument('--output_figure_dir', required=True, type=str, help='Output directory for figures')
-    parser.add_argument('--sample_name', required=True, type=str, help='Name of the sample')
-    parser.add_argument('--trait_name', required=True, type=str, help='Name of the trait')
-    parser.add_argument('--annotation', default=None, type=str, help='Name of the annotation layer.')
-
-
-    # Arguments with defaults
-    parser.add_argument('--fig_title', type=str, default=None, help='Title of figure')
-    parser.add_argument('--fig_height', type=int, default=600, help='Height of figure in pixels')
-    parser.add_argument('--fig_width', type=int, default=800, help='Width of figure in pixels')
-    parser.add_argument('--point_size', type=int, default=None, help='Point size of figure')
-    parser.add_argument('--fig_style', type=str, default='light', choices=['dark', 'light'], help='Plot style of figure')
-
-def add_all_mode_args(parser):
-    parser.add_argument('--input_hdf5_path', required=True, type=str, help='Path to the input hdf5 file.')
-    parser.add_argument('--save_dir', required=True, type=str, help='Path to the running results.')
-    # output
-    # parser.add_argument('--output_hdf5_path', required=True, type=str, help='Path to the output hdf5 file.')
-    parser.add_argument('--sample_name', required=True, type=str, help='Name of the sample.')
-    parser.add_argument('--annotation', default=None, type=str, help='Name of the annotation layer.')
-    parser.add_argument('--type', default=None, type=str, help="The gene expression layer of the input data (e.g., 'count', 'counts', 'log1p').")
-
-    # latent_to_gene
-    # input
-    # parser.add_argument('--input_hdf5_path', type=str, required=True, help='Path to the input HDF5 file.')
-    # parser.add_argument('--sample_name', type=str, required=True, help='Name of the sample.')
-    # output
-    # parser.add_argument('--output_feather_path', type=str, required=True,
-    #                     help='Path to save output gene marker score feather file.')
-    # parser.add_argument('--annotation', default=None, type=str, help='Name of the annotation layer.')
-    # parser.add_argument('--type', default=None, type=str, help="Type of input data (e.g., 'count', 'counts').")
-
-    # no_expression_fraction
-    # no_expression_fraction
-    parser.add_argument('--no_expression_fraction', action='store_true', default=False,
-                        help='Flag to not use expression fraction as filter when calculate the maker score. Default is False.')
-
-    parser.add_argument('--latent_representation', type=str, default='latent_GVAE',
-                        choices=['latent_GVAE', 'latent_PCA'],
-                        help='Type of latent representation. Default is "latent_GVAE".')
-    parser.add_argument('--num_neighbour', type=int, default=21,
-                        help='Number of neighbours to consider. Default is 21.')
-    parser.add_argument('--num_neighbour_spatial', type=int, default=101,
-                        help='Number of spatial neighbours to consider. Default is 101.')
-    parser.add_argument('--species', type=str, default=None, help='Species name, which is the column name in the homolog gene conversion file.')
-    parser.add_argument('--gs_species', type=str, default=None, help='Homologous gene conversion file path, if applicable.')
-    parser.add_argument('--gM_slices', type=str, default=None, help='The mean Gene marker scores path across multiple slices.')
-
-
-    # generate_ldscore
-    # parser.add_argument('--sample_name', type=str, required=True, help='Sample name')
-    # should be all
-    # parser.add_argument('--chrom', type=chrom_choice, required=True, help='Chromosome number (1-22) or "all"')
-    # output
-    # parser.add_argument('--ldscore_save_dir', type=str, required=True, help='Directory to save ld score files')
-
-    # reference panel
-    parser.add_argument('--bfile_root', type=str, required=True, help='Bfile root path')
-    parser.add_argument('--keep_snp_root', type=str, required=True, help='Keep SNP root path')
-
-    # Annotation by gene distance
-    parser.add_argument('--gtf_annotation_file', type=str, required=True, help='GTF file path')
-    parser.add_argument('--gene_window_size', type=int, default=50000, help='Gene window size')
-
-    # Enhancer annotation
-    parser.add_argument('--enhancer_annotation_file', type=str, default=None,
-                        help='Enhancer annotation bed file path, optional.')
-    parser.add_argument('--snp_multiple_enhancer_strategy', type=str, default='max_mkscore',
-                        choices=['max_mkscore', 'nearest_TSS'], help='Strategy for multiple enhancers per SNP')
-    parser.add_argument('--gene_window_enhancer_priority', type=str, default=None,
-                        choices=['gene_window_first', 'enhancer_first', 'enhancer_only'],
-                        help='Priority between gene window and enhancer')
-
-    # Arguments for calculating ld score
-    parser.add_argument('--spots_per_chunk', type=int, default=5_000, 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, default='CM', help='LD window unit (SNP/KB/CM)',
-                        choices=['SNP', 'KB', 'CM'])
-
-    # spatial ldsc args:
-    parser.add_argument('--sumstats_file', default=None, help="Path to GWAS summary statistics file.")
-    parser.add_argument('--sumstats_config_file', default=None, help="Path to GWAS summary statistics config file.")
-    parser.add_argument('--w_file', required=True, help="Path to regression weight file.")
-    parser.add_argument('--ldscore_input_dir', required=True, help="Input directory for LD Score files.")
-    parser.add_argument('--ldsc_save_dir', required=True, help="Directory to save Spatial LDSC results.")
-    parser.add_argument('--trait_name', default=None, help="Name of the trait.")
-    parser.add_argument('--not_M_5_50', action='store_true', help="Flag to not use M 5 50 in calculations.")
-    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('--all_chunk', type=int, help="Number of chunks for processing spatial data.")
-
-
-def get_runall_mode_config(args: argparse.Namespace):
-    # output
-    args.output_hdf5_path = f'{args.save_dir}/{args.sample_name}/find_latent_representations/{args.sample_name}_add_latent.h5ad'
-    args.output_feather_path = f'{args.save_dir}/{args.sample_name}/latent_to_gene/{args.sample_name}_gene_marker_score.feather'
-    args.ldscore_save_dir = f'{args.save_dir}/{args.sample_name}/generate_ldscore'
-    args.ldsc_save_dir = f'{args.save_dir}/{args.sample_name}/spatial_ldsc'
-    args.output_cauchy_dir = f'{args.save_dir}/{args.sample_name}/cauchy_combination/'
-
-    # input
-    args.input_hdf5_with_latent_path = args.output_hdf5_path
-    args.mkscore_feather_file = args.output_feather_path
-    args.ldscore_input_dir = args.ldscore_save_dir
-    args.chrom = 'all'
-    args.input_ldsc_dir = args.ldsc_save_dir
-    args.input_spatial_ldsc = f'{args.save_dir}/{args.sample_name}/spatial_ldsc/{args.sample_name}_{args.trait_name}.gz'
-    # find_latent_representations
-    flr_config = get_dataclass_from_parser(args, FindLatentRepresentationsConfig)
-    # latent_to_gene
-    ltg_config = get_dataclass_from_parser(args, LatentToGeneConfig)
-    # generate_ldscore
-    gls_config = get_dataclass_from_parser(args, GenerateLDScoreConfig)
-    # spatial ldsc
-    ldsc_config = get_dataclass_from_parser(args, SpatialLDSCConfig)
-    # cauchy combination
-    cauchy_config = get_dataclass_from_parser(args, CauchyCombinationConfig)
-    return RunAllModeConfig(flr_config=flr_config, ltg_config=ltg_config, gls_config=gls_config,
-                            ldsc_config=ldsc_config, cauchy_config=cauchy_config)
-
+    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, 
+    parser.add_argument('--sumstats', required=True, type=str,
                         help='Path to gwas summary data')
-    parser.add_argument('--out', required=True, type=str, 
+    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, 
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    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,
+    parser.add_argument('--dbsnp', default=None, type=str,
                         help='Path to reference dnsnp file')
-    parser.add_argument('--chunksize', default=1e+6,type=int,
+    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,
+    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,
+    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')
+                        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='X',
+                        help='Data layer of h5ad for gene expression (e.g., "counts", "log1p", "X").')
+
+    # 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 FindLatentRepresentationsConfig:
-    input_hdf5_path: str
-    output_hdf5_path: str
+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
-    type: str = None
+    data_layer: str = None
 
     epochs: int = 300
     feat_hidden1: int = 256
     feat_hidden2: int = 128
     feat_cell: int = 3000
-    gcn_hidden1: int = 64
-    gcn_hidden2: int = 30
+    gat_hidden1: int = 64
+    gat_hidden2: int = 30
     p_drop: float = 0.1
-    gcn_lr: float = 0.001
+    gat_lr: float = 0.001
     gcn_decay: float = 0.01
     n_neighbors: int = 11
     label_w: float = 1
@@ -413,6 +384,7 @@ class FindLatentRepresentationsConfig:
     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.')
@@ -428,29 +400,43 @@ class FindLatentRepresentationsConfig:
 
 
 @dataclass
-class LatentToGeneConfig:
-    input_hdf5_with_latent_path: str
-    sample_name: str
-    output_feather_path: str
+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
-    species: str = None
-    gs_species: str = None
+    homolog_file: str = None
     gM_slices: str = None
     annotation: str = None
-    type: 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:
-    sample_name: str
+class GenerateLDScoreConfig(ConfigWithAutoPaths):
     chrom: Union[int, str]
-    ldscore_save_dir: str
-    mkscore_feather_file: str
+
     bfile_root: str
-    keep_snp_root: str
+    keep_snp_root: Optional[str]
 
     # annotation by gene distance
     gtf_annotation_file: str
@@ -459,15 +445,28 @@ class GenerateLDScoreConfig:
     # 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
+    gene_window_enhancer_priority: Optional[Literal['gene_window_first', 'enhancer_first', 'enhancer_only',]] = None
 
     # for calculating ld score
-    additional_baseline_annotation_dir_path: str = None
-    spots_per_chunk: int = 5_000
+    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.")
@@ -489,42 +488,55 @@ class GenerateLDScoreConfig:
                 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_dir_path is None:
+        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_dir_path}')
+            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_dir_path) / f'baseline.{chrom}.annot.gz'
+                    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_dir_path}.')
+                        raise FileNotFoundError(
+                            f'baseline.{chrom}.annot.gz is not found in {self.additional_baseline_annotation}.')
             else:
-                baseline_annotation_path = Path(self.additional_baseline_annotation_dir_path) / f'baseline.{self.chrom}.annot.gz'
+                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_dir_path}.')
+                    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:
-    sample_name: str
+class SpatialLDSCConfig(ConfigWithAutoPaths):
     w_file: str
-    ldscore_input_dir: str
-    ldsc_save_dir: str
-    disable_additional_baseline_annotation: bool = False
-    trait_name: str = None
-    sumstats_file: str = None
-    sumstats_config_file: str = None
+    # 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: int = None
-    all_chunk: int = None
+    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:
@@ -540,62 +552,54 @@ class SpatialLDSCConfig:
             with open(self.sumstats_config_file) as f:
                 config = yaml.load(f, Loader=yaml.FullLoader)
             for trait_name, sumstats_file in config.items():
-                self.sumstats_config_dict[trait_name] = sumstats_file
+                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
-        self.process_additional_baseline_annotation()
+        # 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_dir_path = Path(self.ldscore_input_dir) / 'additional_baseline'
-        dir_exists = additional_baseline_annotation_dir_path.exists()
+        additional_baseline_annotation = Path(self.ldscore_save_dir) / 'additional_baseline'
+        dir_exists = additional_baseline_annotation.exists()
 
         if not dir_exists:
-            if self.use_additional_baseline_annotation:
-                logger.warning(f"additional_baseline directory is not found in {self.ldscore_input_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. You should disable use_additional_baseline_annotation')
-            return
-
-        self.use_additional_baseline_annotation = self.use_additional_baseline_annotation or True
-
-        if self.disable_additional_baseline_annotation:
-            logger.warning(
-                f"additional_baseline directory is found in {self.ldscore_input_dir}, but use_additional_baseline_annotation is disabled.")
-            print('''\
-                if you want to use additional baseline annotation,
-                please enable by not adding --disable_additional_baseline_annotation.
-                ''')
             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_dir_path}')
+            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_dir_path / f'baseline.{chrom}.l2.ldscore.feather'
+                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_dir_path}.')
+                        f'baseline.{chrom}.annot.gz is not found in {additional_baseline_annotation}.')
+        return None
 
 
-logger
 @dataclass
-class CauchyCombinationConfig:
-    input_hdf5_path: str
-    input_ldsc_dir: str
-    output_cauchy_dir: str
-    sample_name: str
+class CauchyCombinationConfig(ConfigWithAutoPaths):
     trait_name: str
     annotation: str
     meta: str = None
@@ -603,11 +607,7 @@ class CauchyCombinationConfig:
 
 
 @dataclass
-class VisualizeConfig:
-    input_hdf5_path: str
-    input_ldsc_dir: str
-    output_figure_dir: str
-    sample_name: str
+class VisualizeConfig(ConfigWithAutoPaths):
     trait_name: str
 
     annotation: str = None
@@ -619,12 +619,91 @@ class VisualizeConfig:
 
 
 @dataclass
-class RunAllModeConfig:
-    flr_config: FindLatentRepresentationsConfig
-    ltg_config: LatentToGeneConfig
-    gls_config: GenerateLDScoreConfig
-    ldsc_config: SpatialLDSCConfig
-    cauchy_config: CauchyCombinationConfig
+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
@@ -650,7 +729,7 @@ class FormatSumstatsConfig:
     chunksize: int = 1e+7
     info_min: float = 0.9
     maf_min: float = 0.01
-    keep_chr_pos:bool = False
+    keep_chr_pos: bool = False
 
 
 @register_cli(name='run_find_latent_representations',
@@ -698,37 +777,27 @@ def run_Cauchy_combination_from_cli(args: argparse.Namespace):
     run_Cauchy_combination(config)
 
 
-@register_cli(name='run_visualize',
-              description='Visualize the gsMap results',
-              add_args_function=add_Visualization_args)
-def run_Visualize_from_cli(args: argparse.Namespace):
-    from gsMap.visualize import run_Visualize
-    config = get_dataclass_from_parser(args, VisualizeConfig)
-    run_Visualize(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='run_all_mode',
-              description='Run gsMap method (the full process)',
-              add_args_function=add_all_mode_args)
-def run_all_mode_from_cli(args: argparse.Namespace):
-    from gsMap.find_latent_representation import run_find_latent_representation
-    from gsMap.latent_to_gene import run_latent_to_gene
-    from gsMap.generate_ldscore import run_generate_ldscore
-    from gsMap.spatial_ldsc_multiple_sumstats import run_spatial_ldsc
-    from gsMap.cauchy_combination_test import run_Cauchy_combination
-    config = get_runall_mode_config(args)
-    run_find_latent_representation(config.flr_config)
-    run_latent_to_gene(config.ltg_config)
-    run_generate_ldscore(config.gls_config)
-    run_spatial_ldsc(config.ldsc_config)
-    if args.annotation is not None:
-        config.cauchy_config.annotation = args.annotation
-        run_Cauchy_combination(config.cauchy_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)
+    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)