geney 1.2.67__py2.py3-none-any.whl → 1.2.69__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

@@ -154,7 +154,7 @@ def find_transcript_missplicing_mutid(mut_id):
         for k1, v1 in v.items():
             if abs(v1['delta']) > abs(best_delta):
                 best_delta = v1['delta']
-    return best_delta
+    return out, best_delta
 
 def find_transcript_missplicing(transcript, mutations, context=5000, window=2500, threshold=0.5, engine='spliceai', just_ss=False):
     from functools import reduce

{geney-1.2.67.dist-info → geney-1.2.69.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.67
+Version: 1.2.69
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.67.dist-info → geney-1.2.69.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=faXlBzxohKE02_Jlx6imIP1DKWhGrwQ6mrLldBlqkNU,19218
+geney/splicing_utils.py,sha256=0DFnBJaEqPQ8_0VPFzsXu_ZxaTlw56e0bcAGVLyIH1Q,19223
 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-1.2.67.dist-info/METADATA,sha256=RstIg2k5z5muDUwVglNvZpJQEsMqiXB9jcBaVdvK6S4,948
-geney-1.2.67.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.67.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.67.dist-info/RECORD,,
+geney-1.2.69.dist-info/METADATA,sha256=6Qzw_HkVkPN0J_dFfc8lYuw5rJsIsjKlT_uvybAmltM,948
+geney-1.2.69.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.69.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.69.dist-info/RECORD,,