geney 1.2.31__py2.py3-none-any.whl → 1.2.32__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/seqmat_utils.py +10 -0
  2. {geney-1.2.31.dist-info → geney-1.2.32.dist-info}/METADATA +1 -1
  3. {geney-1.2.31.dist-info → geney-1.2.32.dist-info}/RECORD +5 -5
  4. {geney-1.2.31.dist-info → geney-1.2.32.dist-info}/WHEEL +0 -0
  5. {geney-1.2.31.dist-info → geney-1.2.32.dist-info}/top_level.txt +0 -0
geney/seqmat_utils.py CHANGED
@@ -152,6 +152,16 @@ class SeqMat:
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  padded_subseq = (padding * left_padding) + valid_subseq + (padding * right_padding)
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  return padded_subseq
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+ def asymmetric_indices(self, center, left_context, right_context):
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+ center_idx = np.where(self.seqmat[self.ROW_INDS] == center)[0][0]
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+ start_idx = center_idx - left_context
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+ end_idx = center_idx + right_context + 1 # +1 because end index in slicing is exclusive
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+ left_padding = max(0, -start_idx)
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+ right_padding = max(0, end_idx - len(self.seqmat[self.ROW_INDS]))
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+ valid_start_idx = max(0, start_idx)
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+ valid_end_idx = min(len(self.seqmat[self.ROW_INDS]), end_idx)
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+ valid_subseq = self.indices[valid_start_idx:valid_end_idx]
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+ return valid_subseq
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  def subseq_suffix(self, start):
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  start_pos = np.where(self.seqmat[self.ROW_INDS] == start)[0][0]
{geney-1.2.31.dist-info → geney-1.2.32.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: 1.2.31
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+ Version: 1.2.32
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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-1.2.31.dist-info → geney-1.2.32.dist-info}/RECORD RENAMED
@@ -9,7 +9,7 @@ geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
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  geney/oncosplice.py,sha256=7wf0_-Gkc_G9HhUXjORHk3buZ66JzVzSFVQ4EZOtUAE,21787
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  geney/pangolin_utils.py,sha256=ETTGpuaQgdZ1v8H0NP8sbTEfGWu0VXUFUS7wsURsTc4,2991
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  geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
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- geney/seqmat_utils.py,sha256=jTW2LZEAh5ftgWp0sblq_6AfI21uC4_bPu6zxvLhPWA,17755
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+ geney/seqmat_utils.py,sha256=TDWhE5oVTGJceaO6YmE7I_BEWRxWLT74_3rkmY1M0Fs,18368
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  geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
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  geney/splicing_utils.py,sha256=q47EdcsHrp4aLIPVWvkGBJSzS3l3DKiD9DNDsPpZdHk,16075
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  geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
@@ -19,7 +19,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
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  geney/translation_initiation/tis_utils.py,sha256=iXrWVijyPe-f8I9rEVGdxNnXBrOGPoKFjmvaOEnQYNE,4446
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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-1.2.31.dist-info/METADATA,sha256=vRYAE-ITb5427-B42evqLtx6LOrfhZ7wlGONrlje9vo,948
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- geney-1.2.31.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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- geney-1.2.31.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.2.31.dist-info/RECORD,,
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+ geney-1.2.32.dist-info/METADATA,sha256=aHeSBHWq3b1li4G_CI2ClUEHJc5SfWHowqKrkZbQPGk,948
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+ geney-1.2.32.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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+ geney-1.2.32.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.2.32.dist-info/RECORD,,
{geney-1.2.31.dist-info → geney-1.2.32.dist-info}/WHEEL RENAMED
File without changes