geney 1.2.42__py2.py3-none-any.whl → 1.2.44__py2.py3-none-any.whl

geney/oncosplice.py

@@ -478,7 +478,7 @@ async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=Tr
         assert len(ref_protein) == len(
             cons_vector), f"Protein ({len(ref_protein)}) and conservation vector ({len(cons_vector)} must be same length."
 
-        missplicing = Missplicing(find_transcript_missplicing(transcript, mutations, engine=engine),
+        missplicing = Missplicing(find_transcript_missplicing(transcript, mutations, engine=engine, threshold=splicing_threshold),
                                   threshold=splicing_threshold)
         for mutation in mutations:
             transcript.pre_mrna += mutation
@@ -501,17 +501,21 @@ async def oncosplice_prototype(mut_id, splicing_threshold=0.5, protein_coding=Tr
                 cons_vector))
 
             out = domains_df.apply(lambda row: inspect_domain(row, modified_positions, cons_vector), axis=1)
-            domains_affected = '+'.join([f'{a}:{b}' for a, b in list(zip(out.domain_identifier, out.score))])
+            domains_affected = '+'.join([f'{a}:{round(b, 3)}' for a, b in list(zip(out.domain_identifier, out.score))])
 
             report = OncospliceAnnotator(reference_transcript, transcript, mutation)
             report['mut_id'] = mut_id
             report['oncosplice_score'] = affected_cons_scores
+            report['cons_available'] = transcript.cons_available
+            report['transcript_id'] = transcript.transcript_id
             report['percentile'] = percentile
             report['isoform_id'] = i
             report['isoform_prevalence'] = new_boundaries['path_weight']
             report['full_missplicing'] = missplicing.aberrant_splicing
             report['missplicing'] = max(missplicing)
-            report['domains_affected'] = domains_affected
+            report['domains'] = domains_affected
+            report['max_domain_score'] = out.score.max()
+
             report['reference_resemblance'] = reference_gene_proteins.get(transcript.protein, None)
             results.append(pd.Series(report))
 

{geney-1.2.42.dist-info → geney-1.2.44.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.42
+Version: 1.2.44
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.42.dist-info → geney-1.2.44.dist-info}/RECORD

@@ -6,7 +6,7 @@ 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=vbSmOz3kHFOqJK_qTzWGxKb-FQM2FMZplvz_pbkQGls,23227
+geney/oncosplice.py,sha256=Tmhkswohr6lcagpci26yms_XyXU14V6MqsRcV1XvQaI,23444
 geney/pangolin_utils.py,sha256=lLmnjJdJjqwWS85-1jlPLIjD2z14sWjzU87hS-8xxpQ,2873
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
@@ -20,7 +20,7 @@ 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-1.2.42.dist-info/METADATA,sha256=90jAGKe0wSXZdWOKj87JjFiSiS0Nko9Qg9qWhwgdU5w,948
-geney-1.2.42.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.42.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.42.dist-info/RECORD,,
+geney-1.2.44.dist-info/METADATA,sha256=tVK1pP7jxfft_dc8kghB1pvLShd_C9tsYAL2vGcueAs,948
+geney-1.2.44.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.44.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.44.dist-info/RECORD,,