geney 1.3.41__py2.py3-none-any.whl → 1.3.43__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
 

geney/splicing_utils.py

@@ -413,7 +413,6 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
                 delta2 = m2.get(k, {'delta': 0})['delta'] # max(-1, min(10, m2.get(k, {'delta': 0})['delta'] / ref_val))
                 deltab = mb.get(k, {'delta': 0})['delta'] # max(-1, min(10, mb.get(k, {'delta': 0})['delta'] / ref_val))
 
-                print(event, k, delta1, delta2, deltab)
                 ms1.append(delta1)
                 ms2.append(delta2)
                 msb.append(deltab)
@@ -482,7 +481,7 @@ class Missplicing:
     def __str__(self):
         import pprint
         """String representation displays the filtered splicing events passing the threshold."""
-        return pprint.pprint(self.aberrant_splicing)
+        return pprint.pformat(self.aberrant_splicing)
 
     def __bool__(self):
         """

{geney-1.3.41.dist-info → geney-1.3.43.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.41
+Version: 1.3.43
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.41.dist-info → geney-1.3.43.dist-info}/RECORD

@@ -11,12 +11,12 @@ 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=5NQ_dH-y3Vmdi7d2Vg9-cUPeqByHQiZzY4vovtNp1Q4,23412
+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
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=GFqmGZ-lK5oDook4FZun-mAq-oqZGg6dHZaOdp38B4M,38540
+geney/splicing_utils.py,sha256=TQsRhEegW4SW6t7dghHQ5vGgn9WdioTcai6EzPPcdKM,38485
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -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-1.3.41.dist-info/METADATA,sha256=FJFob_kPTA_y1EwcDjxeL4uncWWv0lrYCT6pKGol61o,990
-geney-1.3.41.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.41.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.41.dist-info/RECORD,,
+geney-1.3.43.dist-info/METADATA,sha256=kqekeyuXWKLb40n_ShUhUqBqqZAyIob5vEDY8dgiSxI,990
+geney-1.3.43.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.43.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.43.dist-info/RECORD,,