gsMap 1.71.2__py3-none-any.whl → 1.73.0__py3-none-any.whl

gsMap/run_all_mode.py

@@ -3,8 +3,15 @@ import time
 from pathlib import Path
 
 from gsMap.cauchy_combination_test import run_Cauchy_combination
-from gsMap.config import GenerateLDScoreConfig, SpatialLDSCConfig, LatentToGeneConfig, \
-    FindLatentRepresentationsConfig, CauchyCombinationConfig, RunAllModeConfig, ReportConfig
+from gsMap.config import (
+    CauchyCombinationConfig,
+    FindLatentRepresentationsConfig,
+    GenerateLDScoreConfig,
+    LatentToGeneConfig,
+    ReportConfig,
+    RunAllModeConfig,
+    SpatialLDSCConfig,
+)
 from gsMap.find_latent_representation import run_find_latent_representation
 from gsMap.generate_ldscore import run_generate_ldscore
 from gsMap.latent_to_gene import run_latent_to_gene
@@ -12,7 +19,6 @@ from gsMap.report import run_report
 from gsMap.spatial_ldsc_multiple_sumstats import run_spatial_ldsc
 
 
-
 def format_duration(seconds):
     hours = int(seconds // 3600)
     minutes = int((seconds % 3600) // 60)
@@ -21,73 +27,94 @@ def format_duration(seconds):
 
 def run_pipeline(config: RunAllModeConfig):
     # # Set up logging
-    log_file = Path(config.workdir) / config.sample_name / 'gsMap_pipeline.log'
+    _current_datatime = time.strftime("%Y%m%d_%H%M%S")
+    log_file = (
+        Path(config.workdir)
+        / config.sample_name
+        / f"gsMap_pipeline_{config.sample_name}_{_current_datatime}.log"
+    )
     log_file.parent.mkdir(parents=True, exist_ok=True)
     logging.basicConfig(
         level=logging.INFO,
-        format='[{asctime}] {levelname:.5s} | {name} - {message}',
+        format="[{asctime}] {levelname:.5s} | {name} - {message}",
         handlers=[
             logging.FileHandler(log_file),
         ],
-        style='{'
+        style="{",
     )
 
-    logger = logging.getLogger('gsMap.pipeline')
+    logger = logging.getLogger("gsMap.pipeline")
     logger.info("Starting pipeline with configuration: %s", config)
+    pipeline_start_time = time.time()
 
-    find_latent_config = FindLatentRepresentationsConfig(
-        workdir=config.workdir,
-        input_hdf5_path=config.hdf5_path,
-        sample_name=config.sample_name,
-        annotation=config.annotation,
-        data_layer=config.data_layer
-    )
+    # Step 1: Find latent representations
+    if config.latent_representation is not None:
+        logger.warning(
+            f"Using the provided latent representation: {config.latent_representation} in {config.hdf5_path}. This would skip the Find_latent_representations step."
+        )
+        logger.info(
+            "Skipping step 1: Find latent representations, as latent representation is provided."
+        )
+        latent_to_gene_input_hdf5_path = config.hdf5_path
+    else:
+        latent_to_gene_input_hdf5_path = None
+        logger.info(
+            "No latent representation provided. Will run the Find_latent_representations step."
+        )
+        find_latent_config = FindLatentRepresentationsConfig(
+            workdir=config.workdir,
+            input_hdf5_path=config.hdf5_path,
+            sample_name=config.sample_name,
+            annotation=config.annotation,
+            data_layer=config.data_layer,
+            n_comps=config.n_comps,
+        )
+
+        # Step 1: Find latent representations
+        start_time = time.time()
+
+        logger.info("Step 1: Finding latent representations")
+        if Path(find_latent_config.hdf5_with_latent_path).exists():
+            logger.info(
+                f"Find latent representations already done. Results saved at {find_latent_config.hdf5_with_latent_path}. Skipping..."
+            )
+        else:
+            run_find_latent_representation(find_latent_config)
+        end_time = time.time()
+        logger.info(f"Step 1 completed in {format_duration(end_time - start_time)}.")
 
     latent_to_gene_config = LatentToGeneConfig(
+        input_hdf5_path=latent_to_gene_input_hdf5_path,
         workdir=config.workdir,
         sample_name=config.sample_name,
         annotation=config.annotation,
-        latent_representation='latent_GVAE',
-        num_neighbour=51,
-        num_neighbour_spatial=201,
-        homolog_file=config.homolog_file
+        latent_representation=config.latent_representation,
+        num_neighbour=config.num_neighbour,
+        num_neighbour_spatial=config.num_neighbour_spatial,
+        homolog_file=config.homolog_file,
+        gM_slices=config.gM_slices,
     )
 
     ldscore_config = GenerateLDScoreConfig(
         workdir=config.workdir,
         sample_name=config.sample_name,
-        chrom='all',
-        # ldscore_save_dir=f"{config.workdir}/{config.sample_name}/generate_ldscore",
-        # mkscore_feather_file=latent_to_gene_config.output_feather_path,
+        chrom="all",
         bfile_root=config.bfile_root,
         keep_snp_root=config.keep_snp_root,
         gtf_annotation_file=config.gtffile,
         spots_per_chunk=5_000,
         baseline_annotation_dir=config.baseline_annotation_dir,
         SNP_gene_pair_dir=config.SNP_gene_pair_dir,
-        ldscore_save_format='quick_mode'
-
+        ldscore_save_format="quick_mode",
     )
 
-    pipeline_start_time = time.time()
-
-    # Step 1: Find latent representations
-    start_time = time.time()
-    logger.info("Step 1: Finding latent representations")
-    if Path(find_latent_config.hdf5_with_latent_path).exists():
-        logger.info(
-            f"Find latent representations already done. Results saved at {find_latent_config.hdf5_with_latent_path}. Skipping...")
-    else:
-        run_find_latent_representation(find_latent_config)
-    end_time = time.time()
-    logger.info(f"Step 1 completed in {format_duration(end_time - start_time)}.")
-
     # Step 2: Latent to gene
     start_time = time.time()
     logger.info("Step 2: Mapping latent representations to genes")
     if Path(latent_to_gene_config.mkscore_feather_path).exists():
         logger.info(
-            f"Latent to gene mapping already done. Results saved at {latent_to_gene_config.mkscore_feather_path}. Skipping...")
+            f"Latent to gene mapping already done. Results saved at {latent_to_gene_config.mkscore_feather_path}. Skipping..."
+        )
     else:
         run_latent_to_gene(latent_to_gene_config)
     end_time = time.time()
@@ -98,9 +125,13 @@ def run_pipeline(config: RunAllModeConfig):
     logger.info("Step 3: Generating LDScores")
 
     # check if LDscore has been generated by the done file
-    ldsc_done_file = Path(ldscore_config.ldscore_save_dir) / f"{config.sample_name}_generate_ldscore.done"
+    ldsc_done_file = (
+        Path(ldscore_config.ldscore_save_dir) / f"{config.sample_name}_generate_ldscore.done"
+    )
     if ldsc_done_file.exists():
-        logger.info(f"Basic LDScore generation already done. Results saved at {ldscore_config.ldscore_save_dir}. Skipping...")
+        logger.info(
+            f"Basic LDScore generation already done. Results saved at {ldscore_config.ldscore_save_dir}. Skipping..."
+        )
     else:
         run_generate_ldscore(ldscore_config)
         end_time = time.time()
@@ -116,11 +147,14 @@ def run_pipeline(config: RunAllModeConfig):
     for trait_name in sumstats_config:
         logger.info("Running spatial LDSC for trait: %s", trait_name)
         # detect if the spatial LDSC has been done:
-        spatial_ldsc_result_file = Path(config.ldsc_save_dir) / f"{config.sample_name}_{trait_name}.csv.gz"
+        spatial_ldsc_result_file = (
+            Path(config.ldsc_save_dir) / f"{config.sample_name}_{trait_name}.csv.gz"
+        )
 
         if spatial_ldsc_result_file.exists():
             logger.info(
-                f"Spatial LDSC already done for trait {trait_name}. Results saved at {spatial_ldsc_result_file}. Skipping...")
+                f"Spatial LDSC already done for trait {trait_name}. Results saved at {spatial_ldsc_result_file}. Skipping..."
+            )
             continue
 
         spatial_ldsc_config_trait = SpatialLDSCConfig(
@@ -132,7 +166,7 @@ def run_pipeline(config: RunAllModeConfig):
             # ldscore_save_dir=spatial_ldsc_config.ldscore_save_dir,
             # ldsc_save_dir=spatial_ldsc_config.ldsc_save_dir,
             num_processes=config.max_processes,
-            ldscore_save_format='quick_mode',
+            ldscore_save_format="quick_mode",
             snp_gene_weight_adata_path=config.snp_gene_weight_adata_path,
         )
         run_spatial_ldsc(spatial_ldsc_config_trait)
@@ -142,13 +176,13 @@ def run_pipeline(config: RunAllModeConfig):
     # Step 5: Cauchy combination test
     start_time = time.time()
     logger.info("Step 6: Running Cauchy combination test")
-    '/storage/yangjianLab/chenwenhao/projects/202312_GPS/test/20240817_vanilla_pipeline_mouse_embryo_v4/E16.5_E1S1.MOSTA/cauchy_combination/E16.5_E1S1.MOSTA_Depression_2023_NatureMed.Cauchy.csv.gz'
     for trait_name in sumstats_config:
         # check if the cauchy combination has been done
         cauchy_result_file = config.get_cauchy_result_file(trait_name)
         if cauchy_result_file.exists():
             logger.info(
-                f"Cauchy combination already done for trait {trait_name}. Results saved at {cauchy_result_file}. Skipping...")
+                f"Cauchy combination already done for trait {trait_name}. Results saved at {cauchy_result_file}. Skipping..."
+            )
             continue
         cauchy_config = CauchyCombinationConfig(
             workdir=config.workdir,
@@ -168,11 +202,18 @@ def run_pipeline(config: RunAllModeConfig):
             sample_name=config.sample_name,
             annotation=config.annotation,
             trait_name=trait_name,
-            plot_type='all',
+            plot_type="all",
             top_corr_genes=50,
             selected_genes=None,
             sumstats_file=sumstats_config[trait_name],
         )
+        gsMap_report_file = report_config.get_gsMap_report_file(trait_name)
+        if Path(gsMap_report_file).exists():
+            logger.info(
+                f"Final report already generated for trait {trait_name}. Results saved at {gsMap_report_file}. Skipping..."
+            )
+            continue
+
         # Create the run parameters dictionary for each trait
         run_parameter_dict = {
             "Sample Name": config.sample_name,
@@ -192,4 +233,4 @@ def run_pipeline(config: RunAllModeConfig):
         # Pass the run parameter dictionary to the report generation function
         run_report(report_config, run_parameters=run_parameter_dict)
 
-    logger.info("Pipeline completed successfully.")
+    logger.info("Pipeline completed successfully.")

gsMap/setup.py

@@ -2,4 +2,4 @@
 import setuptools
 
 if __name__ == "__main__":
-    setuptools.setup(name='gsMap')
+    setuptools.setup(name="gsMap")