geney 1.4.30__py2.py3-none-any.whl → 1.4.31__py2.py3-none-any.whl

geney/utils/spliceai_pytorch_utils.py

@@ -11,29 +11,44 @@ from spliceai_pytorch import SpliceAI
 model = SpliceAI.from_preconfigured('10k')
 
 
+device = torch.device('cpu')
 if sys.platform == 'darwin':
     device = torch.device("mps") if torch.backends.mps.is_available() else torch.device("cpu")
 
 if sys.platform == 'linux':
     device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu")
 
-
 print(f"SpliceAI loaded to {device}.")
 model.to(device)
 
-def one_hot_encode(seq):
 
-    map = np.asarray([[0, 0, 0, 0],
-                      [1, 0, 0, 0],
-                      [0, 1, 0, 0],
-                      [0, 0, 1, 0],
-                      [0, 0, 0, 1]])
+def one_hot_encode(seq: str) -> torch.Tensor:
+    """
+    One-hot encodes a nucleotide sequence into shape [L, 4] (A, C, G, T).
+    Unknowns (N or other) are mapped to all-zero vectors.
+    """
+    map = np.array([
+        [0, 0, 0, 0],  # index 0: unknown (N, etc.)
+        [1, 0, 0, 0],  # A
+        [0, 1, 0, 0],  # C
+        [0, 0, 1, 0],  # G
+        [0, 0, 0, 1],  # T
+    ], dtype=np.float32)
+
+    # Build mapping: ASCII values
+    ascii_seq = np.frombuffer(seq.upper().encode("ascii"), dtype=np.uint8)
 
-    seq = seq.upper().replace('A', '\x01').replace('C', '\x02')
-    seq = seq.replace('G', '\x03').replace('T', '\x04').replace('N', '\x00')
+    # A=65, C=67, G=71, T=84 → map A/C/G/T to 1/2/3/4; others to 0
+    code_map = np.zeros(128, dtype=np.uint8)
+    code_map[ord('A')] = 1
+    code_map[ord('C')] = 2
+    code_map[ord('G')] = 3
+    code_map[ord('T')] = 4
 
-    return map[np.fromstring(seq, np.int8) % 5]
+    indices = code_map[ascii_seq]  # shape [L]
+    onehot = map[indices]          # shape [L, 4]
 
+    return torch.tensor(onehot, dtype=torch.float32)
 
 def sai_predict_probs(seq: str, model) -> list:
     '''
@@ -50,10 +65,12 @@ def sai_predict_probs(seq: str, model) -> list:
     is the donor probability. These probabilities corresponds to the
     middel <L NTs> NTs of the input seq.
     '''
-    x = one_hot_encode(seq)[None, :]
+    x = one_hot_encode(seq)[None, :, :].transpose(1, 2)  # shape: [1, 4, L]
     y = model(x)
-    y = y[0, :, 1:].T
-    return y[0, :], y[1, :]
+    probs = torch.softmax(y, dim=1)  # shape: [1, 3, L]
+    acceptor_probs = probs[0, :, 1]       # [L]
+    donor_probs    = probs[0, :, 2]       # [L]
+    return acceptor_probs.tolist(), donor_probs.tolist()
 
 
 def run_spliceai_seq(seq, indices, threshold=0):

geney/utils/splicing_utils.py

@@ -3,7 +3,6 @@
 import pandas as pd
 from typing import List, Tuple, Optional
 
-# def run_splicing_engine(seq: Optional[str] = None, engine: str = 'spliceai') -> Tuple[List[float], List[float]]:
 def run_splicing_engine(seq: Optional[str] = None, engine: str = 'spliceai') -> Tuple[List[float], List[float]]:
     """
     Run the specified splicing engine to predict splice site probabilities on a sequence.
@@ -25,9 +24,10 @@ def run_splicing_engine(seq: Optional[str] = None, engine: str = 'spliceai') ->
 
     match engine:
         case 'spliceai':
-            # from geney.utils.spliceai_utils import sai_predict_probs, sai_models
-            # acceptor_probs, donor_probs = sai_predict_probs(seq, models=sai_models)
+            from geney.utils.spliceai_utils import sai_predict_probs, sai_models
+            acceptor_probs, donor_probs = sai_predict_probs(seq, models=sai_models)
 
+        case 'spliceai_pytorch':
             from geney.utils.spliceai_pytorch_utils import sai_predict_probs, model
             acceptor_probs, donor_probs = sai_predict_probs(seq, model=model)
 
@@ -41,7 +41,6 @@ def run_splicing_engine(seq: Optional[str] = None, engine: str = 'spliceai') ->
     return donor_probs, acceptor_probs
 
 
-
 def adjoin_splicing_outcomes(splicing_predictions, transcript=None):
     """
     Predicts splicing effect for multiple mutations and organizes the output as a multi-index DataFrame.

{geney-1.4.30.dist-info → geney-1.4.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.30
+Version: 1.4.31
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.30.dist-info → geney-1.4.31.dist-info}/RECORD

@@ -43,11 +43,11 @@ geney/utils/TranscriptLibrary.py,sha256=W1hv4Y8wRlmwTs3iFdn4_IqS-2suVDzZe4fwti2K
 geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
 geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
 geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
-geney/utils/spliceai_pytorch_utils.py,sha256=PfMgaoG6ftWfqKZKc_JNqj5wqQRUR2B-4YF22-zNh1M,2079
+geney/utils/spliceai_pytorch_utils.py,sha256=wwBoT2utKZjjaWAUo11mSoympVK1vkNxAxcJvXAh8SM,2792
 geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
-geney/utils/splicing_utils.py,sha256=Hn7conjcEb3Qc5MTN2DvnlZVxgn3U_IKqOAkGuIik6g,21052
+geney/utils/splicing_utils.py,sha256=joAXSaNdXztKcxR-ZqQ2ypcrnyAc5OQvb-84ODVD0Hs,20965
 geney/utils/utils.py,sha256=GXqlatNhix1akt3fburNzIwhiW9ZdCQSt2vmU80neyA,2370
-geney-1.4.30.dist-info/METADATA,sha256=_DIWzuIrV5xrRCN8VNgctibosZNMXMEVIRsX7d24WNc,990
-geney-1.4.30.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.30.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.30.dist-info/RECORD,,
+geney-1.4.31.dist-info/METADATA,sha256=bMLtt_0GC1DLyBTF0evhQenP8OctQiNSLbe_0awmpqQ,990
+geney-1.4.31.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.4.31.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.31.dist-info/RECORD,,