geney 1.3.7__py2.py3-none-any.whl → 1.3.9__py2.py3-none-any.whl

geney/oncosplice.py

@@ -365,7 +365,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
             report['isoform_id'] = short_hash_of_list(mutated_transcript.exons)
             report['isoform_prevalence'] = new_boundaries['path_weight']
             report['full_missplicing'] = missplicing.aberrant_splicing
-            report['missplicing'] = max(missplicing)
+            report['missplicing'] = missplicing.max_delta()
             report['reference_resemblance'] = reference_gene_proteins.get(mutated_transcript.protein, None)
             results.append(report)
 

geney/splicing_utils.py

@@ -204,7 +204,7 @@ def find_transcript_splicing(transcript, engine: str = 'spliceai') -> Tuple[Dict
     return donor_probs, acceptor_probs
 
 
-def find_transcript_missplicing(mut_id, transcript='primary', threshold=0.5, engine='spliceai', organism='hg38'):
+def find_transcript_missplicing(mut_id, transcript=None, threshold=0.5, engine='spliceai', organism='hg38'):
     gene = Gene.from_file(mut_id.split(':')[0], organism=organism)
     reference_transcript = gene.transcript(transcript) if transcript is not None else gene.transcript()
     variant_transcript = reference_transcript.clone()
@@ -217,7 +217,7 @@ def find_transcript_missplicing(mut_id, transcript='primary', threshold=0.5, eng
     for mutation in mutations:
         variant_transcript.mutate(mutation, inplace=True)
 
-    return find_transcript_missplicing_seqs(reference_transcript.get_context(center, 7500), variant_transcript.get_context(center, 7500), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
+    return find_transcript_missplicing_seqs(reference_transcript.pre_mrna.get_context(center, 7500), variant_transcript.pre_mrna.get_context(center, 7500), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
 
 
     # from functools import reduce
@@ -391,7 +391,7 @@ class Missplicing:
                 yield d['delta']
 
     @property
-    def significant_events(self):
+    def aberrant_splicing(self):
         """
         Returns a filtered version of missplicing events that meet or exceed the current threshold.
         """

{geney-1.3.7.dist-info → geney-1.3.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.7
+Version: 1.3.9
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.7.dist-info → geney-1.3.9.dist-info}/RECORD

@@ -10,12 +10,12 @@ 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=1xphL2LeAObwUKBXgcyyKbNO9bAryKDZesK7OpUpFfA,22336
+geney/oncosplice.py,sha256=LOgpdsTC1JotC2qFnqNMefl0t77vvWCJ5XctZsbrLNA,22343
 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=sDohbrEQx2cevpj6YPPPsfa-ic7R2j6RRpOlbyC5foc,26366
+geney/splicing_utils.py,sha256=YDhYtns6pVHmOfk4Z1AC-acA1kKAqKZmJ-P2EZS946k,26378
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -24,7 +24,7 @@ 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-1.3.7.dist-info/METADATA,sha256=lf_Sup4GRMD5YZZUuIpO0WKbhNX5NBJ53R6AQR5AkfU,994
-geney-1.3.7.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.3.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.7.dist-info/RECORD,,
+geney-1.3.9.dist-info/METADATA,sha256=tkuruBdfjmOTkAz6lM3xZ_nAEXm5Vh4wpaP5FihlTvk,994
+geney-1.3.9.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.3.9.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.9.dist-info/RECORD,,