geney 1.2.12__py2.py3-none-any.whl → 1.2.15__py2.py3-none-any.whl

geney/oncosplice.py

@@ -306,6 +306,7 @@ class Transcript:
         self.cons_vector = ''
         self.variations = None
         self.organism = organism
+        print(f"Variations: {variations}")
         if variations:
             self.variations = Variations(variations)
 
@@ -823,7 +824,7 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
     # print(ref_indices.index(visible_donors[0]), ref_seq_donor_probs[ref_indices.index(visible_donors[0])], mut_seq_donor_probs[mut_indices.index(visible_donors[0])])
 
     print(len(ref_seq_donor_probs), len(ref_seq_acceptor_probs), len(mut_seq_donor_probs), len(mut_seq_acceptor_probs), len(ref_indices), len(mut_indices))
-    print(ref_seq_donor_probs)
+    # print(ref_seq_donor_probs)
 
     assert len(ref_indices) == len(ref_seq_acceptor_probs), 'Reference pos not the same'
     assert len(mut_indices) == len(mut_seq_acceptor_probs), 'Mut pos not the same'
@@ -1040,7 +1041,9 @@ class PredictSpliceAI:
             # elif isinstance(gene_data, Transcript):
 
             # self.missplicing = run_spliceai_transcript(self.modification, transcript_data=gene_data, sai_mrg_context=sai_mrg_context, min_coverage=min_coverage, sai_threshold=0.1)
-            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], variation=mutation, organism='mm39').transcript(gene_data.transcript_id)
+            print("RUNNING")
+            ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], variation=mutation.mut_id, organism='mm39').transcript(gene_data.transcript_id)
+            print(f"Second check : {ref_transcript.pre_mrna == var_transcript.pre_mrna}")
             self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
                                 engine=engine)
             if save_results:

{geney-1.2.12.dist-info → geney-1.2.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.12
+Version: 1.2.15
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.12.dist-info → geney-1.2.15.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
-geney/oncosplice.py,sha256=WgKxl3VbrTKAza65Wci73nEOXtTBN-0TpDjhaKMkeII,77794
+geney/oncosplice.py,sha256=c7OHbgPCDd1ouF3mckGQE-r15xgGJv9hMuabY7ApTMU,77965
 geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
 geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
 geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -45,7 +45,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
 geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney-1.2.12.dist-info/METADATA,sha256=UdmJ2n6dZ4qt2rQ0CR3UzkqVN4g-1wkGos-5pi9PI1Q,1199
-geney-1.2.12.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
-geney-1.2.12.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.12.dist-info/RECORD,,
+geney-1.2.15.dist-info/METADATA,sha256=g6y36w6g8u5eT09QXz0_EEPGxLpVy0OCTLmGe91u2w4,1199
+geney-1.2.15.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
+geney-1.2.15.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.15.dist-info/RECORD,,