geney 1.2.31__py2.py3-none-any.whl → 1.2.33__py2.py3-none-any.whl

geney/seqmat_utils.py

@@ -152,6 +152,16 @@ class SeqMat:
         padded_subseq = (padding * left_padding) + valid_subseq + (padding * right_padding)
         return padded_subseq
 
+    def asymmetric_indices(self, center, left_context, right_context):
+        center_idx = np.where(self.seqmat[self.ROW_INDS] == center)[0][0]
+        start_idx = center_idx - left_context
+        end_idx = center_idx + right_context + 1  # +1 because end index in slicing is exclusive
+        left_padding = max(0, -start_idx)
+        right_padding = max(0, end_idx - len(self.seqmat[self.ROW_INDS]))
+        valid_start_idx = max(0, start_idx)
+        valid_end_idx = min(len(self.seqmat[self.ROW_INDS]), end_idx)
+        valid_subseq = self.indices[valid_start_idx:valid_end_idx]
+        return valid_subseq
 
     def subseq_suffix(self, start):
         start_pos = np.where(self.seqmat[self.ROW_INDS] == start)[0][0]
@@ -193,7 +203,7 @@ class SeqMat:
             return SeqMat('ATG')
 
     def translate(self, tis_index):
-        from Bio import Seq
+        from Bio.Seq import Seq
         return Seq(self.orf_seqmat(tis_index).seq).translate()
 
 

{geney-1.2.31.dist-info → geney-1.2.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.31
+Version: 1.2.33
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.31.dist-info → geney-1.2.33.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
 geney/oncosplice.py,sha256=7wf0_-Gkc_G9HhUXjORHk3buZ66JzVzSFVQ4EZOtUAE,21787
 geney/pangolin_utils.py,sha256=ETTGpuaQgdZ1v8H0NP8sbTEfGWu0VXUFUS7wsURsTc4,2991
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=jTW2LZEAh5ftgWp0sblq_6AfI21uC4_bPu6zxvLhPWA,17755
+geney/seqmat_utils.py,sha256=YV5DFLbfjXLIswPGvqK1-eEfwn9TUby0b2kewdGAKws,18372
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
 geney/splicing_utils.py,sha256=q47EdcsHrp4aLIPVWvkGBJSzS3l3DKiD9DNDsPpZdHk,16075
 geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
@@ -19,7 +19,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=iXrWVijyPe-f8I9rEVGdxNnXBrOGPoKFjmvaOEnQYNE,4446
 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-1.2.31.dist-info/METADATA,sha256=vRYAE-ITb5427-B42evqLtx6LOrfhZ7wlGONrlje9vo,948
-geney-1.2.31.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.31.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.31.dist-info/RECORD,,
+geney-1.2.33.dist-info/METADATA,sha256=MS8m3iEm-fxsKpsoJTNHF8Euari8FVEmwqZJBMn_PL8,948
+geney-1.2.33.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.33.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.33.dist-info/RECORD,,