geney 1.4.15__py2.py3-none-any.whl → 1.4.16__py2.py3-none-any.whl

geney/utils/SeqMats.py

@@ -192,8 +192,8 @@ class SeqMat:
             if len(ref) != len(alt):
                 raise ValueError("Substitution mutations must have alleles of equal length.")
 
-            # pos_idx = np.searchsorted(self.seq_array["index"], pos)
-            pos_idx = self._pos_to_idx.get(pos)
+            pos_idx = np.searchsorted(self.seq_array["index"], pos)
+            # pos_idx = self._pos_to_idx.get(pos)
 
             if pos_idx is None:
                 raise ValueError(f"Position {pos} not found in index")
@@ -202,19 +202,19 @@ class SeqMat:
             if end_idx > len(self.seq_array):
                 raise ValueError(f"Substitution range exceeds sequence length at position {pos}.")
 
-            segment = self.seq_array["ref"][pos_idx:end_idx].tobytes().decode()
-            if segment != ref:
-                raise ValueError(f"Reference mismatch at position {pos}: expected '{ref}', found '{segment}'")
+            # segment = self.seq_array["ref"][pos_idx:end_idx].tobytes().decode()
+            # if segment != ref:
+            #     raise ValueError(f"Reference mismatch at position {pos}: expected '{ref}', found '{segment}'")
 
-            # ref_segment = self.seq_array["ref"][pos_idx:end_idx]
+            ref_segment = self.seq_array["ref"][pos_idx:end_idx]
             # expected_segment = np.frombuffer(ref.encode(), dtype='S1')
-            # if not np.all(ref_segment == np.frombuffer(ref.encode(), dtype='S1')):
-            #     actual_str = ref_segment.tobytes().decode()
-            #     raise ValueError(f"Reference mismatch at position {pos}: expected '{ref}', found '{actual_str}'")
-            # self.seq_array["nt"][pos_idx:end_idx] = np.frombuffer(alt.encode(), dtype='S1')
+            if not np.all(ref_segment == np.frombuffer(ref.encode(), dtype='S1')):
+                actual_str = ref_segment.tobytes().decode()
+                raise ValueError(f"Reference mismatch at position {pos}: expected '{ref}', found '{actual_str}'")
+            self.seq_array["nt"][pos_idx:end_idx] = np.frombuffer(alt.encode(), dtype='S1')
 
-            for i, nt in enumerate(alt):
-                self.seq_array["nt"][pos_idx + i] = nt.encode()
+            # for i, nt in enumerate(alt):
+            #     self.seq_array["nt"][pos_idx + i] = nt.encode()
 
         # Case 2: Insertion (ref is '-' means nothing was present, and we need to add bases)
         elif ref == "-" and alt != "-":

{geney-1.4.15.dist-info → geney-1.4.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.15
+Version: 1.4.16
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.15.dist-info → geney-1.4.16.dist-info}/RECORD

@@ -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=1EgYord9ieaAd1pfAbleBxBnhnubgsNEY9Y40-kVNVo,18502
+geney/utils/SeqMats.py,sha256=syRU5DAuTh3xUfGW_qP9wlcBO5pHsG_y5PlrfXTIxUY,18502
 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-1.4.15.dist-info/METADATA,sha256=6gwA20Ma1aqa3dWNObVhc9fZWQlvsCMzqbKswUl6fTQ,990
-geney-1.4.15.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.15.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.15.dist-info/RECORD,,
+geney-1.4.16.dist-info/METADATA,sha256=xkiO4TiMvtTYt5mdvs2hSOw-ijetjvNf0-MLyX-9poU,990
+geney-1.4.16.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.4.16.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.16.dist-info/RECORD,,