geney 1.3.65__py2.py3-none-any.whl → 1.3.66__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -166,7 +166,7 @@ def run_splicing_engine(seq, engine='spliceai'):
     match engine:
         case 'spliceai':
             from .spliceai_utils import sai_predict_probs, sai_models
-            donor_probs, acceptor_probs = sai_predict_probs(seq, models=sai_models)
+            acceptor_probs, donor_probs = sai_predict_probs(seq, models=sai_models)
 
         case 'pangolin':
             from .pangolin_utils import pangolin_predict_probs, pang_models
@@ -214,6 +214,7 @@ def find_transcript_splicing(transcript, engine: str = 'spliceai') -> Tuple[Dict
     # Create dictionaries and sort them by probability in descending order
     donor_probs = dict(sorted(((i, p) for i, p in zip(ref_indices, ref_seq_donor_probs)),
                        key=lambda item: item[1], reverse=True))
+
     acceptor_probs = dict(sorted(((i, p) for i, p in zip(ref_indices, ref_seq_acceptor_probs)),
                           key=lambda item: item[1], reverse=True))
 
@@ -332,8 +333,8 @@ def find_transcript_missplicing_seqs(ref_seq, var_seq, donors, acceptors, thresh
     if ref_seq.seq == var_seq.seq:
         return Missplicing({'missed_acceptors': {}, 'missed_donors': {}, 'discovered_acceptors': {}, 'discovered_donors': {}})
 
-    ref_seq_acceptor_probs, ref_seq_donor_probs = run_splicing_engine(ref_seq.seq, engine)
-    mut_seq_acceptor_probs, mut_seq_donor_probs = run_splicing_engine(var_seq.seq, engine)
+    ref_seq_donor_probs, ref_seq_acceptor_probs = run_splicing_engine(ref_seq.seq, engine)
+    mut_seq_donor_probs, mut_seq_acceptor_probs = run_splicing_engine(var_seq.seq, engine)
     ref_indices = ref_seq.indices[5000:-5000]
     mut_indices = var_seq.indices[5000:-5000]
     visible_donors = np.intersect1d(donors, ref_indices)

{geney-1.3.65.dist-info → geney-1.3.66.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.65
+Version: 1.3.66
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.65.dist-info → geney-1.3.66.dist-info}/RECORD

@@ -16,7 +16,7 @@ geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=tVY0T6F6l3fNoaktpn7Kq0oH5ZM0ThFYt9nPi_lfakw,3077
-geney/splicing_utils.py,sha256=W-N0ENZJv1PdnVlHuaN_2az2-7Zl6cHYe_CYR1G41U4,40766
+geney/splicing_utils.py,sha256=_nXLCK41GhcrkXHXAqkhNV2IcwFltSxrR-rm8fUIrfE,40767
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
@@ -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-1.3.65.dist-info/METADATA,sha256=L-doIh0XdJuxs4gg1Dhs5mLoa_1zI8_bboq4cnlfvfA,990
-geney-1.3.65.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.65.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.65.dist-info/RECORD,,
+geney-1.3.66.dist-info/METADATA,sha256=bl8lWCBcJsbfBPJmkoY8xG0n6G7z7X1C-6jA1bSevCk,990
+geney-1.3.66.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.66.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.66.dist-info/RECORD,,