geney 1.2.66__py2.py3-none-any.whl → 1.2.68__py2.py3-none-any.whl

geney/seqmat_utils.py

@@ -279,7 +279,18 @@ class Gene:
     @property
     def primary_transcript(self):
         if not hasattr(self, '_primary_transcript'):
-            self._primary_transcript = [k for k, v in self.transcripts.items() if v.get('primary_transcript')][0]
+            primary_transcripts = [k for k, v in self.transcripts.items() if v.get('primary_transcript')]
+            if len(primary_transcripts) > 0:
+                self._primary_transcript = primary_transcripts[0]
+                return self._primary_transcript
+
+            primary_transcripts = [k for k, v in self.transcripts.items() if v.get('transcript_biotype') == 'protein_coding']
+            if len(primary_transcripts) > 0:
+                self._primary_transcript = primary_transcripts[0]
+                return self._primary_transcript
+
+            self._primar_transcript = None
+
         return self._primary_transcript
 
 

geney/splicing_utils.py

@@ -175,7 +175,7 @@ def find_transcript_missplicing(transcript, mutations, context=5000, window=2500
     length = var.seqmat.shape[-1]
     center_index = var.rel_pos(center)
     if center_index is None:
-        raise IndexError, "Center index must not be none... Issue with mutations... They must not be within the transcript."
+        raise IndexError("Center index must not be none... Issue with mutations... They must not be within the transcript.")
     var_start_pad = max(0, total_context - center_index)
     var_end_pad = max(0, total_context - (length - center_index))
 

{geney-1.2.66.dist-info → geney-1.2.68.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.66
+Version: 1.2.68
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.66.dist-info → geney-1.2.68.dist-info}/RECORD

@@ -9,9 +9,9 @@ geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
 geney/oncosplice.py,sha256=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
 geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=prWq3d3rPiyA_evQpY3FP5I-NQFuf7py7Ene8fNZ5DA,19271
+geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=Oj-K4SpMnwnoORBJEB_MHy-K3fGOZlzzWXkFitVaI_I,19218
+geney/splicing_utils.py,sha256=faXlBzxohKE02_Jlx6imIP1DKWhGrwQ6mrLldBlqkNU,19218
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -20,7 +20,7 @@ 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-1.2.66.dist-info/METADATA,sha256=wifLSvv7_r3vXe7n-3XN-8iwWz-PnZrn6OkqYbR-SnM,948
-geney-1.2.66.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.66.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.66.dist-info/RECORD,,
+geney-1.2.68.dist-info/METADATA,sha256=Ircwpep9o4hX8T1-GhKK5WY2nw1rOkLPHJuHMLIPhTE,948
+geney-1.2.68.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.68.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.68.dist-info/RECORD,,