sciv 0.0.97__py3-none-any.whl → 0.0.98__py3-none-any.whl

sciv/model/_core_.py

@@ -15,7 +15,7 @@ from ..tool import RandomWalk, overlap_sum, obtain_cell_cell_network, calculate_
 
 from ..file import save_h5ad, save_pkl, read_h5ad, read_pkl
 from ..preprocessing import filter_data, poisson_vi
-from ..util import path, enrichment_optional, to_dense, collection, to_sparse, difference_peak_optional
+from ..util import path, enrichment_optional, to_dense, collection, to_sparse, difference_peak_optional, project_name
 
 __name__: str = "model_core"
 
@@ -453,7 +453,7 @@ def core(
             model_dir=model_dir
         )
 
-    step1_time = adata.uns["elapsed_time"] + da_peaks.uns["elapsed_time"]
+    poisson_vi_time = adata.uns["elapsed_time"] + da_peaks.uns["elapsed_time"]
 
     if save_path is not None:
 
@@ -485,7 +485,7 @@ def core(
 
     del variants, trait_info
 
-    step2_time = overlap_adata.uns["elapsed_time"]
+    overlap_time = overlap_adata.uns["elapsed_time"]
 
     if save_path is not None and not overlap_is_read:
         save_h5ad(overlap_adata, file=atac_overlap_save_file)
@@ -518,7 +518,7 @@ def core(
 
     del da_peaks, overlap_adata
 
-    step3_time = init_score.uns["elapsed_time"]
+    init_score_time = init_score.uns["elapsed_time"]
 
     if save_path is not None and not init_score_is_read:
         save_h5ad(init_score, file=init_score_save_file)
@@ -546,13 +546,13 @@ def core(
 
     del adata
 
-    step4_time = cc_data.uns["elapsed_time"]
+    smknn_time = cc_data.uns["elapsed_time"]
 
     if save_path is not None and not cc_data_is_read:
         save_h5ad(cc_data, file=cc_data_save_file)
 
     """
-    5. Random walk
+    5. Random walk with weighted seed cells
     """
 
     random_walk_is_read: bool = is_file_exist_loading and os.path.exists(random_walk_save_file) and is_save_random_walk_model
@@ -584,17 +584,29 @@ def core(
     del random_walk_is_read, init_score, cc_data
 
     trs = _run_random_walk_(random_walk, is_ablation, is_simple)
+    trs.uns["params"] = params
+
+    del params
 
-    step5_time = random_walk.elapsed_time
+    random_walk_time = random_walk.elapsed_time
 
     # end time
     elapsed_time = time.time() - start_time
-    step_time = step1_time + step2_time + step3_time + step4_time + step5_time
+    step_time = poisson_vi_time + overlap_time + init_score_time + smknn_time + random_walk_time
 
-    params.update({"elapsed_time": elapsed_time if elapsed_time > step_time else step_time})
-    trs.uns["params"] = params
+    if elapsed_time < step_time:
+        elapsed_time = step_time
 
-    del params
+    ul.log(__name__).info(f"Algorithm {project_name} consumes a total of {elapsed_time} seconds.")
+
+    trs.uns["elapsed_time"] = {
+        "PoissonVI": poisson_vi_time,
+        "Overlap": overlap_time,
+        "initial TRS": init_score_time,
+        "SM-kNN": smknn_time,
+        "Random walk": random_walk_time,
+        "Total time": elapsed_time
+    }
 
     if save_path is not None:
         save_h5ad(trs, file=trs_save_file)

sciv/tool/_algorithm_.py

@@ -993,7 +993,7 @@ def overlap_sum(regions: AnnData, variants: dict, trait_info: DataFrame, n_jobs:
 
     # Use Parallel to process traits in parallel
     results = Parallel(n_jobs=n_jobs)(
-        delayed(_process_trait_)(trait_name, col_idx) for col_idx, trait_name in enumerate(trait_names)
+        delayed(_process_trait_)(trait_name, col_idx) for col_idx, trait_name in tqdm(enumerate(trait_names))
     )
 
     # Preallocate length to avoid list dynamic expansion
@@ -1234,10 +1234,18 @@ def calculate_init_score_weight(
 
     ul.log(__name__).info("Calculate initial trait relevance scores")
     _init_trs_weight_ = np.multiply(_init_trs_ncw_, _cell_type_weight_)
+
+    if hasattr(_init_trs_weight_, "A"):
+        _init_trs_weight_ = _init_trs_weight_.A
+
     init_trs_adata = AnnData(_init_trs_weight_, obs=cell_anno, var=trait_anno)
     del _init_trs_weight_
 
     if not is_simple:
+
+        if hasattr(_init_trs_ncw_, "A"):
+            _init_trs_ncw_ = _init_trs_ncw_.A
+
         init_trs_adata.layers["init_trs_ncw"] = _init_trs_ncw_
         init_trs_adata.layers["cell_type_weight"] = to_sparse(_cell_type_weight_)
         init_trs_adata.uns["cluster_weight_factor"] = da_peaks_adata.obsm["cluster_weight"]

{sciv-0.0.97.dist-info → sciv-0.0.98.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: sciv
-Version: 0.0.97
+Version: 0.0.98
 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-0.0.97.dist-info → sciv-0.0.98.dist-info}/RECORD

@@ -3,7 +3,7 @@ sciv/file/__init__.py,sha256=8cYLG0S0nilblmyX46CWFrbLr-rmLbO1EEO477pZ-gk,520
 sciv/file/_read_.py,sha256=UZJpN3_5hBiTjzEYO6YXORcE_dqA8HmLpV80nqTLNSo,30554
 sciv/file/_write_.py,sha256=W3M9CmPi7BuKAffz1fdi-vA5DzAFZ7wmcggp33N9Xtg,7848
 sciv/model/__init__.py,sha256=k8SO9FpJaGn2ANqJyaz3HXMas7jH9toPVtpw703kOqg,149
-sciv/model/_core_.py,sha256=rKIEhVz67HM7hXkEUpUR9l7uyIK72jK1zANPVpB_Hcc,33277
+sciv/model/_core_.py,sha256=HCXPFOxfed5TUJMI-pZV9cx9_2R8z4dNPb2f7Hp3mVc,33693
 sciv/plot/__init__.py,sha256=2tRNT6TZNz9r38lnna712RGsH7OJ2QkGa37XKgzejHQ,1865
 sciv/plot/_bar_.py,sha256=xWpFbJTHgQMLuUSXa4uE69RGHXSCGinapxL-1imdDcU,14355
 sciv/plot/_barcode_.py,sha256=RDOedQ8ZtXWFyJ2c772RDfqO4TMIpHMvcMZMAVqky90,5073
@@ -27,13 +27,13 @@ sciv/preprocessing/_scanpy_.py,sha256=tB8BD2wpLAU8_YxdqrgNtcjpNXNRo-JCdm2lxaKDBL
 sciv/preprocessing/_scvi_.py,sha256=7QxwPA2kR_g15X28aEak7AFA4kyQ-UbtpiLH-rc5Ksg,10780
 sciv/preprocessing/_snapatac_.py,sha256=Dq8CHF7Psl3CQszaEokQYO56Oe2uzyWOy_cGlaOywfc,27798
 sciv/tool/__init__.py,sha256=WXzHkWt6RgBC3qqD-98nR5wQmt6oC850ox_VpMrapSU,2468
-sciv/tool/_algorithm_.py,sha256=BzUUBn22R12PoQHSjhcKZfj6Yw01Qh_VIgl8RXgWvfY,53580
+sciv/tool/_algorithm_.py,sha256=mYKfSuYGelLd2secwyqGPxBQYd3x2yDKw1z7HK8mqYE,53773
 sciv/tool/_matrix_.py,sha256=SnC3sXic_ufuEXStcD_HncvYH6apBdNK6nhG6jFLmjA,24324
 sciv/tool/_random_walk_.py,sha256=JOB97XLxlZYHvlIST1wlXgA0mw6fybkWnJGq6X_kbsk,48871
 sciv/util/__init__.py,sha256=nOxZ8if27X7AUJ6hZwTwxOJwIBJb0obWlHjqCzjg_Gc,1964
 sciv/util/_constant_.py,sha256=w0wKQd8guLd1ZTW24_5aECrWsIWDiNQmEpLsWlHar1A,3000
 sciv/util/_core_.py,sha256=TUWfBNRJzWuoQ9ffew_DjnlkNydG-Rmujl_RH4Ln9io,14917
-sciv-0.0.97.dist-info/METADATA,sha256=lCXJ0ySEYDpLmHDMuR7FXcg5bEKA_THBDG1aCqH7Siw,3465
-sciv-0.0.97.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-sciv-0.0.97.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
-sciv-0.0.97.dist-info/RECORD,,
+sciv-0.0.98.dist-info/METADATA,sha256=yZiAx2el-OqapNmZNjUpjAmTAmQbIcBIZa7QFXjYPYc,3465
+sciv-0.0.98.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+sciv-0.0.98.dist-info/licenses/LICENSE,sha256=4UvHVf3qCOZjHLs4LkYz8u96XRpXnZrpTKrkUQPs5_A,1075
+sciv-0.0.98.dist-info/RECORD,,