geney 1.3.21__py2.py3-none-any.whl → 1.3.23__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -218,20 +218,19 @@ def find_transcript_missplicing(mut_id, transcript=None, threshold=0.5, engine='
     if db is not None:
         cached_data = db.get_mutation_data(engine, gene.gene_name, mut_id, reference_transcript.transcript_id)
         if cached_data and not force_recompute:
-            return cached_data
+            return Missplicing(cached_data)
 
     variant_transcript = reference_transcript.clone()
     mutations = [MutSeqMat.from_mutid(m) for m in mut_id.split('|')]
     mutations = [m for m in mutations if m in reference_transcript]
     if len(mutations) == 0:
-        return {'missed_acceptors': {}, 'missed_donors': {}, 'discovered_acceptors': {}, 'discovered_donors': {}}
+        return Missplicing({'missed_acceptors': {}, 'missed_donors': {}, 'discovered_acceptors': {}, 'discovered_donors': {}})
 
     center = np.mean([m.indices[0] for m in mutations]) // 1
     for mutation in mutations:
         variant_transcript.mutate(mutation, inplace=True)
 
     missplicing = find_transcript_missplicing_seqs(reference_transcript.pre_mrna.get_context(center, 7500, padding='N'), variant_transcript.pre_mrna.get_context(center, 7500, padding='N'), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
-
     if db is not None:
         db.store_mutation_data(engine, gene.gene_name, mut_id, reference_transcript.transcript_id, missplicing.missplicing)
 

{geney-1.3.21.dist-info → geney-1.3.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.21
+Version: 1.3.23
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.21.dist-info → geney-1.3.23.dist-info}/RECORD

@@ -16,7 +16,7 @@ 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=FLBmVglyALQbu3SEBq9VaKtRjqWabudvTz0jvPtJEuA,35538
+geney/splicing_utils.py,sha256=mA2IgLx0gXi4IFzB1bIaoai1nLC34M-IOcgqcDUaivI,35563
 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-1.3.21.dist-info/METADATA,sha256=I-cnugoCjWnQJSG7GVvr_xD8D3mPgIdLADpAvBsSJfk,971
-geney-1.3.21.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.21.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.21.dist-info/RECORD,,
+geney-1.3.23.dist-info/METADATA,sha256=1kzW2OTgrk2DJK2TZGxQvYZ47Rm1KSsTsDu7F4uCRnA,971
+geney-1.3.23.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.23.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.23.dist-info/RECORD,,