geney 1.4.28__py2.py3-none-any.whl → 1.4.30__py2.py3-none-any.whl

geney/utils/splicing_utils.py

@@ -1,9 +1,10 @@
 # __all__ = ['run_splicing_engine', 'adjoin_splicing_outcomes', 'process_epistasis']
 
 import pandas as pd
-from typing import List, Tuple
+from typing import List, Tuple, Optional
 
-def run_splicing_engine(seq: str, engine: str = 'spliceai') -> Tuple[List[float], List[float]]:
+# 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.
 
@@ -17,12 +18,19 @@ def run_splicing_engine(seq: str, engine: str = 'spliceai') -> Tuple[List[float]
     Raises:
         ValueError: If the engine is not implemented.
     """
+
+    if seq is None:
+        from geney.utils.utils import generate_random_sequence
+        seq = generate_random_sequence(15_000)
+
     match engine:
         case 'spliceai':
-            from geney.utils.spliceai_utils import sai_predict_probs, sai_models
+            # 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_pytorch_utils import sai_predict_probs, model
-            # print(seq)
-            acceptor_probs, donor_probs = sai_predict_probs(seq, models=model)
+            acceptor_probs, donor_probs = sai_predict_probs(seq, model=model)
+
         case 'pangolin':
             from geney.utils.pangolin_utils import pangolin_predict_probs, pang_models
             # print(seq)

geney/utils/utils.py

@@ -6,6 +6,7 @@ import json
 # from pathlib import Path
 from bisect import bisect_left
 import hashlib
+import random
 
 # def is_monotonic(A):
 #     x, y = [], []
@@ -60,6 +61,9 @@ def is_monotonic(A):
     return all(x <= y for x, y in zip(A, A[1:])) or all(x >= y for x, y in zip(A, A[1:]))
 
 
+def generate_random_sequence(length: int) -> str:
+    """Generates a random DNA sequence of given length (A, C, G, T)."""
+    return ''.join(random.choices('ACGT', k=length))
 
 def generate_random_nucleotide_sequences(num_sequences, min_len=3, max_len=10):
     """

{geney-1.4.28.dist-info → geney-1.4.30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.28
+Version: 1.4.30
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.28.dist-info → geney-1.4.30.dist-info}/RECORD

@@ -45,9 +45,9 @@ geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw
 geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
 geney/utils/spliceai_pytorch_utils.py,sha256=PfMgaoG6ftWfqKZKc_JNqj5wqQRUR2B-4YF22-zNh1M,2079
 geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
-geney/utils/splicing_utils.py,sha256=pg5UnlGPaVgV3mw1GUzC-J-bDC1EtjTgkWsqtN-XVMM,20714
-geney/utils/utils.py,sha256=m51Vd0cEbrcIHo6_8BAuI9YSPcKRs22e5LfVd2Qj6Is,2181
-geney-1.4.28.dist-info/METADATA,sha256=q7DMJSJXyJ2IJ1qQD8xofQ4f2-cZZi6TvTUmEvfbyaA,990
-geney-1.4.28.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.28.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.28.dist-info/RECORD,,
+geney/utils/splicing_utils.py,sha256=Hn7conjcEb3Qc5MTN2DvnlZVxgn3U_IKqOAkGuIik6g,21052
+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,,