smftools 0.1.7__py3-none-any.whl → 0.2.3__py3-none-any.whl

smftools/tools/__init__.py

@@ -1,49 +1,20 @@
-from .apply_hmm import apply_hmm
-from .apply_hmm_batched import apply_hmm_batched
-from .position_stats import calculate_relative_risk_on_activity, compute_positionwise_statistic
-from .calculate_distances import calculate_distances
+from .position_stats import calculate_relative_risk_on_activity, compute_positionwise_statistics
 from .calculate_umap import calculate_umap
-from .call_hmm_peaks import call_hmm_peaks
-from .classifiers import run_training_loop, run_inference, evaluate_models_by_subgroup, prepare_melted_model_data, sliding_window_train_test
 from .cluster_adata_on_methylation import cluster_adata_on_methylation
-from .display_hmm import display_hmm
 from .general_tools import create_nan_mask_from_X, combine_layers, create_nan_or_non_gpc_mask
-from .hmm_readwrite import load_hmm, save_hmm
-from .nucleosome_hmm_refinement import refine_nucleosome_calls, infer_nucleosomes_in_large_bound
 from .read_stats import calculate_row_entropy
+from .spatial_autocorrelation import *
 from .subset_adata import subset_adata
-from .train_hmm import train_hmm
 
-from . import models
-from . import data
-from . import utils
-from . import evaluation
-from . import inference
-from . import training
 
 __all__ = [
-    "apply_hmm",
-    "apply_hmm_batched",
-    "calculate_distances",
-    "compute_positionwise_statistic",
+    "compute_positionwise_statistics",
     "calculate_row_entropy",
     "calculate_umap",
     "calculate_relative_risk_on_activity",
-    "call_hmm_peaks",
     "cluster_adata_on_methylation",
     "create_nan_mask_from_X",
     "create_nan_or_non_gpc_mask",
     "combine_layers",
-    "display_hmm",
-    "evaluate_models_by_subgroup",
-    "load_hmm",
-    "prepare_melted_model_data",
-    "refine_nucleosome_calls",
-    "infer_nucleosomes_in_large_bound",
-    "run_training_loop",
-    "run_inference",
-    "save_hmm",
-    "sliding_window_train_test"
     "subset_adata",
-    "train_hmm"
 ]

smftools/tools/calculate_umap.py

@@ -10,10 +10,10 @@ def calculate_umap(adata, layer='nan_half', var_filters=None, n_pcs=15, knn_neig
     if var_filters:
         subset_mask = np.logical_or.reduce([adata.var[f].values for f in var_filters])
         adata_subset = adata[:, subset_mask].copy()
-        print(f"🔹 Subsetting adata: Retained {adata_subset.shape[1]} features based on filters {var_filters}")
+        print(f"Subsetting adata: Retained {adata_subset.shape[1]} features based on filters {var_filters}")
     else:
         adata_subset = adata.copy()
-        print("🔹 No var filters provided. Using all features.")
+        print("No var filters provided. Using all features.")
 
     # Step 2: NaN handling inside layer
     if layer:
@@ -24,9 +24,9 @@ def calculate_umap(adata, layer='nan_half', var_filters=None, n_pcs=15, knn_neig
                 data = np.nan_to_num(data, nan=0.5)
                 adata_subset.layers[layer] = data
             else:
-                print("✅ No NaNs detected.")
+                print("No NaNs detected.")
         else:
-            print("✅ Sparse matrix detected; skipping NaN check (sparse formats typically do not store NaNs).")
+            print("Sparse matrix detected; skipping NaN check (sparse formats typically do not store NaNs).")
 
     # Step 3: PCA + neighbors + UMAP on subset
     if "X_umap" not in adata_subset.obsm or overwrite:
@@ -57,6 +57,6 @@ def calculate_umap(adata, layer='nan_half', var_filters=None, n_pcs=15, knn_neig
     adata.varm["PCs"] = pc_matrix
 
 
-    print(f"✅ Stored: adata.obsm['X_pca'] and adata.obsm['X_umap']")
+    print(f"Stored: adata.obsm['X_pca'] and adata.obsm['X_umap']")
 
     return adata

smftools/tools/general_tools.py

@@ -5,7 +5,7 @@ def create_nan_mask_from_X(adata, new_layer_name="nan_mask"):
     import numpy as np
     nan_mask = np.isnan(adata.X).astype(int)
     adata.layers[new_layer_name] = nan_mask
-    print(f"✅ Created '{new_layer_name}' layer based on NaNs in adata.X")
+    print(f"Created '{new_layer_name}' layer based on NaNs in adata.X")
     return adata
 
 def create_nan_or_non_gpc_mask(adata, obs_column, new_layer_name="nan_or_non_gpc_mask"):
@@ -22,7 +22,7 @@ def create_nan_or_non_gpc_mask(adata, obs_column, new_layer_name="nan_or_non_gpc
     mask = np.maximum(nan_mask, combined_mask)
     adata.layers[new_layer_name] = mask
 
-    print(f"✅ Created '{new_layer_name}' layer based on NaNs in adata.X and non-GpC regions using {obs_column}")
+    print(f"Created '{new_layer_name}' layer based on NaNs in adata.X and non-GpC regions using {obs_column}")
     return adata
 
 def combine_layers(adata, input_layers, output_layer, negative_mask=None, values=None, binary_mode=False):
@@ -64,6 +64,6 @@ def combine_layers(adata, input_layers, output_layer, negative_mask=None, values
         combined[mask == 0] = 0
 
     adata.layers[output_layer] = combined
-    print(f"✅ Combined layers into {output_layer} {'(binary)' if binary_mode else f'with values {values}'}")
+    print(f"Combined layers into {output_layer} {'(binary)' if binary_mode else f'with values {values}'}")
 
     return adata