geney 1.3.40__py2.py3-none-any.whl → 1.3.42__py2.py3-none-any.whl

geney/oncosplice.py

@@ -329,7 +329,7 @@ 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:
+        if '*' in reference_transcript.protein or len(reference_transcript.protein) < window_length:
             print(f"> Errors in reference transcript {reference_transcript.transcript_id}")
             continue
 
@@ -344,18 +344,18 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
         else:
             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.gene_name, transcript_id=reference_transcript.transcript_id)
+                missplicing = Missplicing(splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene.gene_name, transcript_id=reference_transcript.transcript_id))
                 no_splicing_record = missplicing is None
 
             if missplicing is None:
-                missplicing = Missplicing(find_transcript_missplicing_seqs(
+                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))
+                    reference_transcript.acceptors, threshold=splicing_threshold, engine=splicing_engine)
                 if no_splicing_record and splicing_db is not None:
                     splicing_db.store_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene.gene_name, transcript_id=reference_transcript.transcript_id, data=missplicing.missplicing)
 
-        alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing.aberrant_splicing)
+        alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing.missplicing)
         for i, new_boundaries in enumerate(alternative_splicing_paths):
             mutated_transcript.acceptors = new_boundaries['acceptors']
             mutated_transcript.donors = new_boundaries['donors']

{geney-1.3.40.dist-info → geney-1.3.42.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.40
+Version: 1.3.42
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.40.dist-info → geney-1.3.42.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=El0urUlm5LEfVdG2B13laiD9meLTjsr0ajugIygihLg,23418
+geney/oncosplice.py,sha256=6s0aW6vXtD-z7yToFBcFCS5M_npoQe4tgdf4g5TuR2o,23465
 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-1.3.40.dist-info/METADATA,sha256=VZhSxq_zulnOeWI7ZV1EbWoXlsk_x0PAG7klGfJUpc4,990
-geney-1.3.40.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.40.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.40.dist-info/RECORD,,
+geney-1.3.42.dist-info/METADATA,sha256=T03j-Q8uS4YIhmyJDA4SxYH_1k6nMZvd98tM1ElEpAM,990
+geney-1.3.42.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.42.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.42.dist-info/RECORD,,