geney 1.3.67__py2.py3-none-any.whl → 1.3.69__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

@@ -602,7 +602,6 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
 
     # Further filter acceptors: keep only columns where the value in the second row is < 0.1.
     # (Assumes that the second row (iloc[1]) represents a specific measure you wish to threshold.)
-    acceptors_df = acceptors_df.loc[:, acceptors_df.iloc[1] < 0.1]
 
     # Helper function: add new features (residual and deviations) and filter based on residual.
     def add_features_and_filter(df):
@@ -626,10 +625,16 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
     acceptors_df = add_features_and_filter(acceptors_df)
 
     # Return the processed dataframes with the new features persisting.
-    donors_df.loc['site_type', :] = 0
-    acceptors_df.loc['site_type', :] = 1
+    if donors_df.shape[1] > 0:
+        donors_df.loc['site_type', :] = 0
+    if acceptors_df.shape[1] > 0:
+        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
@@ -637,6 +642,7 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
         ),
         axis=0
     )
+
     df.loc['synergistic'] = 0
     df.loc['synergistic', mask] = 1
 

{geney-1.3.67.dist-info → geney-1.3.69.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.67
+Version: 1.3.69
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.67.dist-info → geney-1.3.69.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=afnTncU607dLLfMz4Z1pj06dkO03u6Wt43cNBu7pEjU,47647
+geney/splicing_utils.py,sha256=50Cmn12BEzvCQfDe-8u4lNVkqhNn2FXI_Q0Nw98MKBo,47699
 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-1.3.67.dist-info/METADATA,sha256=Quhz5RoxRIVxv0VlKP9NhmIdy0NzcOi3viZ51WIBzm8,990
-geney-1.3.67.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.67.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.67.dist-info/RECORD,,
+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,,