tpcav 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

tpcav/cavs.py

@@ -409,8 +409,11 @@ def run_tpcav(
     output_dir: str = "tpcav/",
     num_samples_for_pca=10,
     num_samples_for_cav=1000,
+    input_window_length=1024,
+    batch_size=8,
     bws=None,
     input_transform_func=helper.fasta_chrom_to_one_hot_seq,
+    p=4
 ):
     """
     One-stop function to compute CAVs on motif concepts and bed concepts, compute AUC of motif concept f-scores after correction
@@ -427,12 +430,12 @@ def run_tpcav(
     for nm in num_motif_insertions:
         builder = ConceptBuilder(
             genome_fasta=genome_fasta,
-            input_window_length=1024,
+            input_window_length=input_window_length,
             bws=bws,
             num_motifs=nm,
             include_reverse_complement=True,
             min_samples=num_samples_for_cav,
-            batch_size=8,
+            batch_size=batch_size,
         )
         # use random regions as control
         builder.build_control()
@@ -449,12 +452,12 @@ def run_tpcav(
     if bed_seq_file is not None or bed_chrom_file is not None:
         bed_builder = ConceptBuilder(
             genome_fasta=genome_fasta,
-            input_window_length=1024,
+            input_window_length=input_window_length,
             bws=bws,
             num_motifs=0,
             include_reverse_complement=True,
             min_samples=num_samples_for_cav,
-            batch_size=8,
+            batch_size=batch_size,
         )
         # use random regions as control
         bed_builder.build_control()
@@ -493,7 +496,7 @@ def run_tpcav(
                 [motif_concept,],
                 num_samples_for_cav,
                 output_dir=str(output_path / f"cavs_{nm}_motifs/"),
-                num_processes=4,
+                num_processes=p,
             )
         motif_cav_trainers[nm] = cav_trainer
     if bed_builder is not None:
@@ -505,7 +508,7 @@ def run_tpcav(
             bed_builder.concepts,
             num_samples_for_cav,
             output_dir=str(output_path / f"cavs_bed_concepts/"),
-            num_processes=4,
+            num_processes=p,
         )
     else:
         bed_cav_trainer = None

{tpcav-0.2.0.dist-info → tpcav-0.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tpcav
-Version: 0.2.0
+Version: 0.2.1
 Summary: Testing with PCA projected Concept Activation Vectors
 Author-email: Jianyu Yang <yztxwd@gmail.com>
 License-Expression: MIT AND (Apache-2.0 OR BSD-2-Clause)

{tpcav-0.2.0.dist-info → tpcav-0.2.1.dist-info}/RECORD

@@ -1,12 +1,12 @@
 tpcav/__init__.py,sha256=CpHijSyE1HMy8dlvdSaYrwN9gYMGDEJGDdsneNWnqdA,996
-tpcav/cavs.py,sha256=lqw-V45FCiCNUC8w7payuSPsbMBFy_qcOZaqPGA68js,19195
+tpcav/cavs.py,sha256=qXeNiTqlrCPb824ivVvZNrhHSZ6YRx2xmjdZ9JTlAgM,19299
 tpcav/concepts.py,sha256=_ht4UTu2EVJh52JGnKT3PEgDHk4Q-JCpNuHfFOVmzCw,12884
 tpcav/helper.py,sha256=CcNFJEFG00pujUrthBoMInpIBz1mWIG3y5fztaiHO-c,9917
 tpcav/logging_utils.py,sha256=wug7O_5IjxjhOpQr-aq90qKMEUp1EgcPkrv26d8li6Q,281
 tpcav/tpcav_model.py,sha256=XgNLPXr6_B-Dyb7RdgsUsFnrSK6oNjqqFPOjpz1wXmM,16564
 tpcav/utils.py,sha256=s2TfC-YoH_xa73WuMqvtpuqzx6g3ne12hE90Yg9hToY,21502
-tpcav-0.2.0.dist-info/licenses/LICENSE,sha256=uC-2s0ObLnQzWFKH5aokHXo6CzxlJgeI0P3bIUCZgfU,1064
-tpcav-0.2.0.dist-info/METADATA,sha256=tz5MWTr_-veczwEOPDGUzLEwy3XU9WLlSw4IPOzddc0,3502
-tpcav-0.2.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
-tpcav-0.2.0.dist-info/top_level.txt,sha256=I9veSE_WsuFYrXlcfRevqtatDyWWZNsWA3dV0CeBXVg,6
-tpcav-0.2.0.dist-info/RECORD,,
+tpcav-0.2.1.dist-info/licenses/LICENSE,sha256=uC-2s0ObLnQzWFKH5aokHXo6CzxlJgeI0P3bIUCZgfU,1064
+tpcav-0.2.1.dist-info/METADATA,sha256=XaYcUWr6humOfiUhwgKrccufSqDl_XiAutlO_wCf4lo,3502
+tpcav-0.2.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+tpcav-0.2.1.dist-info/top_level.txt,sha256=I9veSE_WsuFYrXlcfRevqtatDyWWZNsWA3dV0CeBXVg,6
+tpcav-0.2.1.dist-info/RECORD,,