geney 1.3.69__py2.py3-none-any.whl → 1.3.71__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -631,31 +631,31 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
         acceptors_df.loc['site_type', :] = 1
 
     df = pd.concat([acceptors_df, donors_df], axis=1)
-
-    if df.shape[1] == 0:
-        return df
-
-    mask = df.apply(
-        lambda col: (
-                (abs(col['residual']) > 0.1) and
-                (abs(col['deviation1'] + col['deviation2']) < 0.1)
-        ),
-        axis=0
-    )
-
-    df.loc['synergistic'] = 0
-    df.loc['synergistic', mask] = 1
-
-    mask = df.apply(
-        lambda col: (
-                (abs(col['residual']) > 0.1) and
-                (abs(col['total_deviation']) <= 0.25)
-        ),
-        axis=0
-    )
-
-    df.loc['antagonistic'] = 0
-    df.loc['antagonistic', mask] = 1
+    #
+    # if df.shape[1] == 0:
+    #     return df
+    #
+    # mask = df.apply(
+    #     lambda col: (
+    #             (abs(col['residual']) > 0.1) and
+    #             (abs(col['deviation1'] + col['deviation2']) < 0.1)
+    #     ),
+    #     axis=0
+    # )
+    #
+    # df.loc['synergistic'] = 0
+    # df.loc['synergistic', mask] = 1
+    #
+    # mask = df.apply(
+    #     lambda col: (
+    #             (abs(col['residual']) > 0.1) and
+    #             (abs(col['total_deviation']) <= 0.25)
+    #     ),
+    #     axis=0
+    # )
+    #
+    # df.loc['antagonistic'] = 0
+    # df.loc['antagonistic', mask] = 1
     df.loc['mut_id'] = mid
     df.loc['engine'] = engine
     df.loc['site'] = df.columns
@@ -800,7 +800,7 @@ class Missplicing:
 def benchmark_splicing(gene, organism='hg38', engine='spliceai'):
     gene = Gene(gene, organism=organism)
     transcript = gene.transcript()
-    if len(transcript.introns) == 0:
+    if transcript is None or len(transcript.introns) == 0:
         return None, None
 
     transcript.generate_pre_mrna()

{geney-1.3.69.dist-info → geney-1.3.71.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.69
+Version: 1.3.71
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.69.dist-info → geney-1.3.71.dist-info}/RECORD

@@ -16,7 +16,7 @@ geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=tVY0T6F6l3fNoaktpn7Kq0oH5ZM0ThFYt9nPi_lfakw,3077
-geney/splicing_utils.py,sha256=50Cmn12BEzvCQfDe-8u4lNVkqhNn2FXI_Q0Nw98MKBo,47699
+geney/splicing_utils.py,sha256=-4Xd7durnm3362IYn_7RO7dOZkPRadWZcRZgvTF2Thg,47786
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
@@ -25,7 +25,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
-geney-1.3.69.dist-info/METADATA,sha256=TP1TKZ9MHD4j7Lwm7yDe7YpRcrKh3blSiBvmrmpxTmo,990
-geney-1.3.69.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.69.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.69.dist-info/RECORD,,
+geney-1.3.71.dist-info/METADATA,sha256=qwuLQNso5Kv8Xs23-90MykN695SOLmAkMbpaco1FbhM,990
+geney-1.3.71.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.71.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.71.dist-info/RECORD,,