sciv 0.0.80__py3-none-any.whl → 0.0.82__py3-none-any.whl

sciv/tool/_algorithm_.py

@@ -1023,7 +1023,10 @@ def calculate_fragment_weighted_accessibility(input_data: dict, block_size: int
 
     ul.log(__name__).info("Calculate expected counts matrix ===> (numerator)")
     global_scale_data = vector_multiply_block_storage(row_sum, col_sum, block_size=block_size)
-    global_scale_data = global_scale_data.astype(np.float32)
+
+    if block_size <= 0:
+        global_scale_data = global_scale_data.astype(np.float32)
+
     del row_sum, col_sum
 
     global_scale_data /= all_sum * 1.0
@@ -1034,7 +1037,7 @@ def calculate_fragment_weighted_accessibility(input_data: dict, block_size: int
     overlap_matrix = to_dense(overlap_matrix)
     global_scale_data = global_scale_data.dot(overlap_matrix)
 
-    global_scale_data[global_scale_data != 0] = global_scale_data[global_scale_data != 0].min() / 2
+    global_scale_data[global_scale_data == 0] = global_scale_data[global_scale_data != 0].min() / 2
 
     ul.log(__name__).info("Calculate fragment weighted accessibility.")
     init_score = to_dense(init_score)
@@ -1127,7 +1130,10 @@ def calculate_init_score_weight(
 
     ul.log(__name__).info("Calculate expected counts matrix ===> (numerator)")
     global_scale_data = vector_multiply_block_storage(row_sum, col_sum, block_size=block_size)
-    global_scale_data = global_scale_data.astype(np.float32)
+
+    if block_size <= 0:
+        global_scale_data = global_scale_data.astype(np.float32)
+
     del row_sum, col_sum
 
     global_scale_data /= all_sum * 1.0
@@ -1139,7 +1145,7 @@ def calculate_init_score_weight(
     global_scale_data = global_scale_data.dot(overlap_matrix)
     del overlap_matrix
 
-    global_scale_data[global_scale_data != 0] = global_scale_data[global_scale_data != 0].min() / 2
+    global_scale_data[global_scale_data == 0] = global_scale_data[global_scale_data != 0].min() / 2
 
     ul.log(__name__).info("Calculate fragment weighted accessibility.")
     _init_trs_ncw_ = to_dense(_init_trs_ncw_)
@@ -1147,7 +1153,7 @@ def calculate_init_score_weight(
 
     del global_scale_data
 
-    da_peaks_adata.obsm["cluster_weight"] = to_sparse(_cluster_weight_)
+    da_peaks_adata.obsm["cluster_weight"] = to_dense(_cluster_weight_, is_array=True)
     del _cluster_weight_
 
     ul.log(__name__).info("Broadcasting the weight factor to the cellular level")
@@ -1157,9 +1163,7 @@ def calculate_init_score_weight(
 
     for cluster in da_peaks_adata.obs_names:
         mask = cluster_series == cluster
-        _cell_type_weight_[mask, :] = to_dense(
-            da_peaks_adata[cluster, :].obsm["cluster_weight"], is_array=True
-        ).flatten().astype(np.float32)
+        _cell_type_weight_[mask, :] = da_peaks_adata[cluster, :].obsm["cluster_weight"].flatten().astype(np.float32)
 
     ul.log(__name__).info("Calculate initial trait relevance scores")
     _init_trs_weight_ = np.multiply(_init_trs_ncw_, _cell_type_weight_)

sciv/tool/_matrix_.py

@@ -449,10 +449,10 @@ def matrix_operation_memory_efficient(
             result_chunk = chunk1.multiply(chunk2)
         elif operation == '/':
             # Sparse matrix division: convert to dense, perform element-wise division, then convert back to sparse
-            dense_chunk1 = chunk1.todense()
+            dense_chunk1 = chunk1 if isinstance(chunk1, dense_data) else chunk1.todense()
 
             if isinstance(data2, matrix_data):
-                dense_chunk2 = chunk2.todense()
+                dense_chunk2 = chunk2 if isinstance(chunk2, dense_data) else chunk2.todense()
                 dense_chunk2[dense_chunk2 == 0] = default
             else:
                 dense_chunk2 = data2

{sciv-0.0.80.dist-info → sciv-0.0.82.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.80
+Version: 0.0.82
 Summary: Unveiling the pivotal cell types involved in variant function regulation at a single-cell resolution
 Project-URL: github, https://github.com/YuZhengM/sciv
 Author-email: Zheng-Min Yu <yuzmbio@163.com>

{sciv-0.0.80.dist-info → sciv-0.0.82.dist-info}/RECORD

@@ -27,13 +27,13 @@ sciv/preprocessing/_scanpy_.py,sha256=mmkk4cMCzJCziF49RnOuXBiF4frS6aSiwZdUmfDAg4
 sciv/preprocessing/_scvi_.py,sha256=ZIDkQ_4deYmzSMiAbu5C3j_jMMl7hBTFLCBXHCNj3B4,10332
 sciv/preprocessing/_snapatac_.py,sha256=Dq8CHF7Psl3CQszaEokQYO56Oe2uzyWOy_cGlaOywfc,27798
 sciv/tool/__init__.py,sha256=WXzHkWt6RgBC3qqD-98nR5wQmt6oC850ox_VpMrapSU,2468
-sciv/tool/_algorithm_.py,sha256=ggMW1tWxojQElbZcSdugHwwOm68KGFvuujtV7Zg-n4A,48003
-sciv/tool/_matrix_.py,sha256=NDQf7yTuN4_GaKL7jK5i1BGYCIOGFQHcmpWgQkuquK8,24230
+sciv/tool/_algorithm_.py,sha256=6xLGB1-FRfRiHSCVb_tHvzY_N-RoMZ79p0O2fEio688,48030
+sciv/tool/_matrix_.py,sha256=O1EAhA9wxh06P_eOxEBesK7kO7IExKlhH6uJzGh1HBM,24322
 sciv/tool/_random_walk_.py,sha256=98HLa9X2xx3Tj7VKKwQ2oS-CWL7HbOURAXiYKky2OYs,47338
 sciv/util/__init__.py,sha256=nOxZ8if27X7AUJ6hZwTwxOJwIBJb0obWlHjqCzjg_Gc,1964
 sciv/util/_constant_.py,sha256=w0wKQd8guLd1ZTW24_5aECrWsIWDiNQmEpLsWlHar1A,3000
 sciv/util/_core_.py,sha256=ZD2uSnEBHVu0i9TmXWzri_3bXZzYKnIZk818gW3zadE,14751
-sciv-0.0.80.dist-info/METADATA,sha256=YIURiNcqDzxUamWuaHg89UIvX4rsDHR4XrKs4S6jAMQ,3465
-sciv-0.0.80.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-sciv-0.0.80.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
-sciv-0.0.80.dist-info/RECORD,,
+sciv-0.0.82.dist-info/METADATA,sha256=JTluLyVcmc6vYfTh76ejiHiT0fnqSEVJa9XngVEGj2U,3465
+sciv-0.0.82.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+sciv-0.0.82.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
+sciv-0.0.82.dist-info/RECORD,,