geney 1.4.9__py2.py3-none-any.whl → 1.4.11__py2.py3-none-any.whl

geney/Gene.py

@@ -1,6 +1,6 @@
 import copy
 # import random
-# from . import config
+from . import config
 from typing import Any, Dict, List, Tuple, Optional, Iterator, Union, TYPE_CHECKING
 from collections import Counter
 from .utils.utils import unload_pickle

geney/utils/SeqMats.py

@@ -149,6 +149,9 @@ class SeqMat:
         cloned.version = self.version
         cloned.notes = self.notes.copy()
         cloned.rev = self.rev
+
+        cloned._pos_to_idx = {pos: i for i, pos in enumerate(cloned.seq_array["index"])}
+
         return cloned
 
     def apply_mutation(self, pos: int, ref: str, alt: str, only_snps: bool = False):
@@ -193,7 +196,7 @@ class SeqMat:
             pos_idx = self._pos_to_idx.get(pos)
             if pos_idx is None:
                 raise ValueError(f"Position {pos} not found in index")
-            
+
             end_idx = pos_idx + len(ref)
             if end_idx > len(self.seq_array):
                 raise ValueError(f"Substitution range exceeds sequence length at position {pos}.")

{geney-1.4.9.dist-info → geney-1.4.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.9
+Version: 1.4.11
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.9.dist-info → geney-1.4.11.dist-info}/RECORD

@@ -1,5 +1,5 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
-geney/Gene.py,sha256=gJN9nPJJT_l4qdHqSoMB36YYKVs5gBvQ9tBJsVsYMgs,7038
+geney/Gene.py,sha256=6x1sEZV50Il4oydegW6iHIF12EZTGexniG3YUD-3DfM,7036
 geney/Oncosplice.py,sha256=ETAvMl_Oq6mEJQHPNwdDO5csX6Ahuped_om10KifCyM,17739
 geney/SeqMats.py,sha256=9-eJnfU2w3LGc0XvVvFEO_QrBneTkC6xkZKDfTcEw5o,19282
 geney/SpliceSimulator.py,sha256=iF6feVeSnsKFmn3WV60CgWLI0_rSLgpq5fVFL1IOv_4,18491
@@ -37,7 +37,7 @@ geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4w
 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/utils/Fasta_segment.py,sha256=weB5NJ65P0XiyAJCiCHx4T9sHC1pWLpuQeOy0B85gyg,11364
-geney/utils/SeqMats.py,sha256=kpv5v_6VgUc72Qip3fLYZV_7Jb6dIoQLIrECL5BCBl4,18207
+geney/utils/SeqMats.py,sha256=Kwyr8rylSKVSjnrxRTvZ5IrutRQgeD9CKUaqsKkFASk,18286
 geney/utils/TranscriptLibrary.py,sha256=ma_ZVPgglxXDDneEvdqxxeqxG8eSFL-zgLUXyC6BqY8,2070
 geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
 geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
@@ -45,7 +45,7 @@ geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M
 geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
 geney/utils/splicing_utils.py,sha256=vPCGnCPR1ooEZEHR79yFHLmRQXEJHXEQjjxpBR-YWOs,20635
 geney/utils/utils.py,sha256=m51Vd0cEbrcIHo6_8BAuI9YSPcKRs22e5LfVd2Qj6Is,2181
-geney-1.4.9.dist-info/METADATA,sha256=iTeevxIYdU6A8rP1j77OwH0mZ1m0rjrrTKHtYn8PnKo,989
-geney-1.4.9.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.9.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.9.dist-info/RECORD,,
+geney-1.4.11.dist-info/METADATA,sha256=fvC01VxWlv5gOeNf-ZFt1rNvjXAxHEGYf0prneQUDR8,990
+geney-1.4.11.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.4.11.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.11.dist-info/RECORD,,