gsMap 1.73.3__py3-none-any.whl → 1.73.4__py3-none-any.whl

gsMap/__init__.py

@@ -2,4 +2,4 @@
 Genetics-informed pathogenic spatial mapping
 """
 
-__version__ = "1.73.3"
+__version__ = "1.73.4"

gsMap/config.py

@@ -972,10 +972,7 @@ class GenerateLDScoreConfig(ConfigWithAutoPaths):
     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
+    ldscore_save_format: Literal["feather", "quick_mode"] = "feather"
 
     # for pre calculating the SNP Gene ldscore Weight
     save_pre_calculate_snp_gene_weight_matrix: bool = False
@@ -1059,10 +1056,6 @@ class GenerateLDScoreConfig(ConfigWithAutoPaths):
                         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):
@@ -1079,7 +1072,7 @@ class SpatialLDSCConfig(ConfigWithAutoPaths):
     all_chunk: int | None = None
     chunk_range: tuple[int, int] | None = None
 
-    ldscore_save_format: Literal["feather", "zarr", "quick_mode"] = "feather"
+    ldscore_save_format: Literal["feather", "quick_mode"] = "feather"
 
     spots_per_chunk_quick_mode: int = 1_000
     snp_gene_weight_adata_path: str | None = None

gsMap/diagnosis.py

@@ -9,6 +9,7 @@ from scipy.stats import norm
 
 from gsMap.config import DiagnosisConfig
 from gsMap.utils.manhattan_plot import ManhattanPlot
+from gsMap.utils.regression_read import _read_chr_files
 from gsMap.visualize import draw_scatter, estimate_point_size_for_plot, load_ldsc, load_st_coord
 
 warnings.filterwarnings("ignore", category=FutureWarning)
@@ -100,10 +101,11 @@ def load_gwas_data(config: DiagnosisConfig):
 def load_snp_gene_pairs(config: DiagnosisConfig):
     """Load SNP-gene pairs from multiple chromosomes."""
     ldscore_save_dir = Path(config.ldscore_save_dir)
+    snp_gene_pair_file_prefix = ldscore_save_dir / "SNP_gene_pair/SNP_gene_pair_chr"
     return pd.concat(
         [
-            pd.read_feather(ldscore_save_dir / f"SNP_gene_pair/SNP_gene_pair_chr{chrom}.feather")
-            for chrom in range(1, 23)
+            pd.read_feather(file)
+            for file in _read_chr_files(snp_gene_pair_file_prefix.as_posix(), suffix=".feather")
         ]
     )
 
@@ -168,7 +170,6 @@ def generate_manhattan_plot(config: DiagnosisConfig):
 
     # Log some diagnostic information
     logger.info(f"Creating Manhattan plot with {len(gwas_data_to_plot)} SNPs")
-    logger.info(f"Columns available: {list(gwas_data_to_plot.columns)}")
     logger.info(f"Chromosome column values: {gwas_data_to_plot['CHR'].unique()}")
 
     fig = ManhattanPlot(