geney 1.3.37__py2.py3-none-any.whl → 1.3.39__py2.py3-none-any.whl

geney/Gene.py

@@ -78,6 +78,10 @@ class Gene:
         for tid, annotations in self.transcripts.items():
             yield Transcript(annotations, organism=self.organism)
 
+    def __getitem__(self, item):
+        print(f"{item} not an annotated transcript of this gene.")
+        return Transcript(self.transcripts[item], organism=self.organism) if item in self.transcripts else None
+
     @classmethod
     def from_file(cls, gene_name, organism='hg38'):
         # Load data from file here

geney/Transcript.py

@@ -371,7 +371,7 @@ class Transcript:
             return self if inplace else ("", np.array([]))
 
         # Translate the ORF to protein
-        protein = str(Seq(self.orf.seq).translate()).replace('*', '')
+        protein = str(Seq(self.orf.seq).translate()).strip('*') # .replace('*', '')
 
         # Use existing cons_vector or default to an array of ones
         self.cons_vector = self.cons_vector if hasattr(self, 'cons_vector') and len(self.cons_vector) == len(protein) else np.ones(len(protein))

geney/oncosplice.py

@@ -329,6 +329,10 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
             mutated_transcript.mutate(mutation, inplace=True)
 
         reference_transcript.generate_mature_mrna().generate_protein()
+        if '*' in reference_transcript.protein:
+            print(f"> Errors in reference transcript {reference_transcript.transcript_id}")
+            continue
+
         reference_transcript.cons_vector = transform_conservation_vector(reference_transcript.cons_vector,
                                                                          window=window_length)
 

{geney-1.3.37.dist-info → geney-1.3.39.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.37
+Version: 1.3.39
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.37.dist-info → geney-1.3.39.dist-info}/RECORD

@@ -1,7 +1,7 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
-geney/Gene.py,sha256=1pqKI3hGZndi7VY4j66ObhJjnz8YiNtBLGJTIHWVujA,6670
+geney/Gene.py,sha256=nMWJjoQaiVFm2iRjoiq7ghZqnXtW0tJDcq2S0AyOIvY,6883
 geney/SeqMats.py,sha256=aLpqd7RJSEU07jdPXpbtZPeb2D9BxrZuW6BTkcXpNE4,18819
-geney/Transcript.py,sha256=s2QtC5IGAJNZ1Uf3S-eTCzTXy6lrDzXbxb9pcLMwbQg,14485
+geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
 geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
 geney/allele_linkage.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -11,7 +11,7 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
-geney/oncosplice.py,sha256=GNxbofZ84aEU9MxmV223S2AzT4ZxFe3azumX0sKImYs,23243
+geney/oncosplice.py,sha256=if9C_7s7tjA-6QQXXxKM2VGExdUwJfnNtsxsFsUf36g,23405
 geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
@@ -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-1.3.37.dist-info/METADATA,sha256=s_ozaSGvJtbWOKfF7vTyJSa0UjUm_ssmf5YOdGQQ_Yw,990
-geney-1.3.37.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.37.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.37.dist-info/RECORD,,
+geney-1.3.39.dist-info/METADATA,sha256=UOJiSEnmTP4xI_JhYkGoswQivS9UuEhotKkASjo8l8c,990
+geney-1.3.39.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.39.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.39.dist-info/RECORD,,