geney 1.4.10__py2.py3-none-any.whl → 1.4.11__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/utils/SeqMats.py +4 -1
  2. {geney-1.4.10.dist-info → geney-1.4.11.dist-info}/METADATA +1 -1
  3. {geney-1.4.10.dist-info → geney-1.4.11.dist-info}/RECORD +5 -5
  4. {geney-1.4.10.dist-info → geney-1.4.11.dist-info}/WHEEL +0 -0
  5. {geney-1.4.10.dist-info → geney-1.4.11.dist-info}/top_level.txt +0 -0
geney/utils/SeqMats.py CHANGED
@@ -149,6 +149,9 @@ class SeqMat:
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  cloned.version = self.version
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  cloned.notes = self.notes.copy()
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  cloned.rev = self.rev
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+
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+ cloned._pos_to_idx = {pos: i for i, pos in enumerate(cloned.seq_array["index"])}
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+
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  return cloned
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  def apply_mutation(self, pos: int, ref: str, alt: str, only_snps: bool = False):
@@ -193,7 +196,7 @@ class SeqMat:
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  pos_idx = self._pos_to_idx.get(pos)
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  if pos_idx is None:
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  raise ValueError(f"Position {pos} not found in index")
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-
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+
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  end_idx = pos_idx + len(ref)
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  if end_idx > len(self.seq_array):
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  raise ValueError(f"Substitution range exceeds sequence length at position {pos}.")
{geney-1.4.10.dist-info → geney-1.4.11.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: geney
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- Version: 1.4.10
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+ Version: 1.4.11
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  Summary: A Python package for gene expression modeling.
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  Home-page: https://github.com/nicolaslynn/geney
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  Author: Nicolas Lynn
{geney-1.4.10.dist-info → geney-1.4.11.dist-info}/RECORD RENAMED
@@ -37,7 +37,7 @@ geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4w
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  geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
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  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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  geney/utils/Fasta_segment.py,sha256=weB5NJ65P0XiyAJCiCHx4T9sHC1pWLpuQeOy0B85gyg,11364
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- geney/utils/SeqMats.py,sha256=kpv5v_6VgUc72Qip3fLYZV_7Jb6dIoQLIrECL5BCBl4,18207
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+ geney/utils/SeqMats.py,sha256=Kwyr8rylSKVSjnrxRTvZ5IrutRQgeD9CKUaqsKkFASk,18286
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  geney/utils/TranscriptLibrary.py,sha256=ma_ZVPgglxXDDneEvdqxxeqxG8eSFL-zgLUXyC6BqY8,2070
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  geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
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  geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
@@ -45,7 +45,7 @@ geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M
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  geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
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  geney/utils/splicing_utils.py,sha256=vPCGnCPR1ooEZEHR79yFHLmRQXEJHXEQjjxpBR-YWOs,20635
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  geney/utils/utils.py,sha256=m51Vd0cEbrcIHo6_8BAuI9YSPcKRs22e5LfVd2Qj6Is,2181
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- geney-1.4.10.dist-info/METADATA,sha256=sC6GeWBSkBjO3TiAdksz4Xs0SZEx-gGwpf9Eu-s8q6w,990
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- geney-1.4.10.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.4.10.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.4.10.dist-info/RECORD,,
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+ geney-1.4.11.dist-info/METADATA,sha256=fvC01VxWlv5gOeNf-ZFt1rNvjXAxHEGYf0prneQUDR8,990
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+ geney-1.4.11.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.4.11.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.4.11.dist-info/RECORD,,
{geney-1.4.10.dist-info → geney-1.4.11.dist-info}/WHEEL RENAMED
File without changes