geney 1.2.63__py2.py3-none-any.whl → 1.2.65__py2.py3-none-any.whl

geney/seqmat_utils.py

@@ -78,7 +78,15 @@ class SeqMat:
         #                                                                                     :].max() >= mut_seqmat[
         #                                                                                                 self.ROW_INDS,
         #                                                                                                 :].max(), 'Mutation outside sequence'
-        assert np.all(np.isin(mut_seqmat[1, :], ref_seqmat[1, :])), "Mutation not in sequence"
+        # assert np.all(np.isin(mut_seqmat[1, :], ref_seqmat[1, :])), "Mutation not in sequence"
+        if not np.all(np.isin(mut_seqmat[1, :], ref_seqmat[1, :])):
+            if return_seqmat:
+                return ref_seqmat
+
+            return ''.join(self.vectorized_map_v2c(ref_seqmat[self.ROW_SEQ, :])), ref_seqmat[self.ROW_INDS,
+                                                                                  :], ref_seqmat[
+                                                                                      self.ROW_SUPERINDS,
+                                                                                      :]
 
         if np.any(mut_seqmat[self.ROW_SUPERINDS, :] > 0):
             insertions = np.where(mut_seqmat[self.ROW_SUPERINDS, :] > 0)[0][0]
@@ -175,7 +183,10 @@ class SeqMat:
         return SeqMat().set_seqmat(self.seqmat[:, max(0, condition - context):min(self.seqmat.shape[-1], condition + context + 1)])
 
     def rel_pos(self, pos):
-        return np.where(self.seqmat[1, :] == pos)[0][0]
+        if pos in self.indices:
+            return np.where(self.seqmat[1, :] == pos)[0][0]
+        else:
+            return None
 
     def orf_seqmat(self, tis_index):
         if tis_index not in self.seqmat[1, :]:

{geney-1.2.63.dist-info → geney-1.2.65.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.63
+Version: 1.2.65
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.63.dist-info → geney-1.2.65.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
 geney/oncosplice.py,sha256=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
 geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=f-4dtufdKHc52jf_xZqbwBu-DXCa2Tl0Wsigguus6-E,18661
+geney/seqmat_utils.py,sha256=prWq3d3rPiyA_evQpY3FP5I-NQFuf7py7Ene8fNZ5DA,19271
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
 geney/splicing_utils.py,sha256=nYfdM-ppHS1kUrwzDcS6VHxpHGv3vVl4p7f_JWKZTL8,18831
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
@@ -20,7 +20,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 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-1.2.63.dist-info/METADATA,sha256=LKx_Q2GIKC23LqLmz6Qb6LvymWRXcKXjkJX8BItRzgM,948
-geney-1.2.63.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.63.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.63.dist-info/RECORD,,
+geney-1.2.65.dist-info/METADATA,sha256=hoHzB0bxM3dkqxFgl0xaTZCBphhIBu33bN6D-lgQHrw,948
+geney-1.2.65.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.65.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.65.dist-info/RECORD,,