geney 1.3.68__py2.py3-none-any.whl → 1.3.70__py2.py3-none-any.whl

geney/Gene.py

@@ -1,4 +1,5 @@
 import copy
+import random
 from typing import Any, Dict, List, Tuple, Optional, Iterator, Union, TYPE_CHECKING
 from collections import Counter
 from . import unload_pickle, config
@@ -143,7 +144,8 @@ class Gene:
             tid = self.primary_transcript
 
         if tid is None:
-            return Transcript()
+            tid = random.choice(list(self.transcripts.keys()))
+            return None #Transcript()
 
         if tid not in self.transcripts:
             raise AttributeError(f"Transcript '{tid}' not found in gene '{self.gene_name}'.")

geney/splicing_utils.py

@@ -631,34 +631,34 @@ 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
-    df.loc['mut_id'] = mid
-    df.loc['engine'] = engine
-    df.loc['site'] = df.columns
+    #
+    # 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
     df = df.rename({mid: 'epistasis', mid.split('|')[0]: 'cv1', mid.split('|')[1]: 'cv2'})
     df = df.T
     return df
@@ -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-1.3.68.dist-info → geney-1.3.70.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.68
+Version: 1.3.70
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.68.dist-info → geney-1.3.70.dist-info}/RECORD

@@ -1,5 +1,5 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
-geney/Gene.py,sha256=nMWJjoQaiVFm2iRjoiq7ghZqnXtW0tJDcq2S0AyOIvY,6883
+geney/Gene.py,sha256=oAdwuguD1qWMTrS158ApW4s3MRcb1ZJlinzVeCZcYwE,6966
 geney/SeqMats.py,sha256=9-eJnfU2w3LGc0XvVvFEO_QrBneTkC6xkZKDfTcEw5o,19282
 geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
@@ -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=JKQvm-4uJesSIe6_i6UAwhZfojJFGhXv5ZxvrwWy_54,47792
 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-1.3.68.dist-info/METADATA,sha256=kREzXHGHU6MjvTQCSgq9o3csVnm28mktBzx8WeUYtX8,990
-geney-1.3.68.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.68.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.68.dist-info/RECORD,,
+geney-1.3.70.dist-info/METADATA,sha256=4n6FWqVc4DONBOKNmhWZ5RMCik7GMPz8F4l8O5nbcjo,990
+geney-1.3.70.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.70.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.70.dist-info/RECORD,,