geney 1.3.34__py2.py3-none-any.whl → 1.3.35__py2.py3-none-any.whl

geney/oncosplice.py

@@ -338,18 +338,20 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
         if splicing_engine is None:
             missplicing = Missplicing()
         else:
-            missplicing = None
+            missplicing, no_splicing_record = None, True
             if splicing_db is not None:
                 missplicing = splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene, transcript_id=reference_transcript.transcript_id)
+                no_splicing_record = missplicing is None
 
             if missplicing is None:
                 missplicing = find_transcript_missplicing_seqs(
                     reference_transcript.pre_mrna.get_context(center, context=7500, padding='N'),
                     mutated_transcript.pre_mrna.get_context(center, context=7500, padding='N'), reference_transcript.donors,
                     reference_transcript.acceptors, threshold=splicing_threshold, engine=splicing_engine)
+                if no_splicing_record and splicing_db is not None:
+                    splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene, transcript_id=reference_transcript.transcript_id, data=missplicing.missplicing)
 
         alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing.aberrant_splicing)
-
         for i, new_boundaries in enumerate(alternative_splicing_paths):
             mutated_transcript.acceptors = new_boundaries['acceptors']
             mutated_transcript.donors = new_boundaries['donors']
@@ -384,7 +386,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
     return pd.DataFrame(results)[
         ['mut_id', 'transcript_id', 'isoform_id', 'primary_transcript', 'missplicing', 'full_missplicing',
          'exon_changes', 'splicing_codes', 'affected_exon', 'affected_intron', 'mutation_distance_from_5',
-         'mutation_distance_from_3', 'engine', 'reference_resemblance', 'oncosplice_score', 'percentile',
+         'mutation_distance_from_3', 'reference_resemblance', 'oncosplice_score', 'percentile',
          'isoform_prevalence', 'reference_protein', 'variant_protein', 'splicing_engine']]
 
 #

{geney-1.3.34.dist-info → geney-1.3.35.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.34
+Version: 1.3.35
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.34.dist-info → geney-1.3.35.dist-info}/RECORD

@@ -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=_YprtZRsY5bxibCYG3aLKcuFrT4YopgzN8vuF1Bt1IE,22902
+geney/oncosplice.py,sha256=3_XAUbzpCTYBI9W1uag75ed93lsNw8UuvnM6LjwTXZY,23221
 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-1.3.34.dist-info/METADATA,sha256=Q4zzmf9fGDfPR6feyGgtKJIwSakMtMSjJ88cT9hErvs,990
-geney-1.3.34.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.34.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.34.dist-info/RECORD,,
+geney-1.3.35.dist-info/METADATA,sha256=yhGQQBVx7g7hjOBXPgMZMb5-R9gfnnpjFVNWnRJuPwQ,990
+geney-1.3.35.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.35.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.35.dist-info/RECORD,,