geney 1.2.25__py2.py3-none-any.whl → 1.2.27__py2.py3-none-any.whl

geney/seqmat_utils.py

@@ -145,8 +145,8 @@ class SeqMat:
         return self.seqmat[:, start_pos:]
 
     def subseq_prefix(self, end):
-        start_pos = np.where(self.seqmat[self.ROW_INDS] == end)[0][0]
-        return self.seqmat[:, :end]
+        end_pos = np.where(self.seqmat[self.ROW_INDS] == end)[0][0]
+        return self.seqmat[:, :end_pos]
 
     def inspect(self, pos, context=500):
         condition = np.where(self.seqmat[1, :] == pos)[0][0]
@@ -161,16 +161,17 @@ class SeqMat:
 
         temp = SeqMat().set_seqmat(self.subseq_suffix(tis_index))
         # Ensure the sequence length is divisible by 3
-        seq_length = len(temp.seq)
+        # seq_length = len(temp.seq)
 
-        if seq_length % 3 != 0:
-            temp.seqmat = temp.seqmat[:, :-(seq_length % 3)]  # Trim the extra nucleotides
+        # if seq_length % 3 != 0:
+        #     temp.seqmat = temp.seqmat[:, :-(seq_length % 3)]  # Trim the extra nucleotides
 
         if temp.seq[:3] == 'ATG':
             for i in range(3, len(temp.seq), 3):
                 codon = temp.seq[i:i + 3]
                 if codon in ['TAA', 'TAG', 'TGA']:
                     index = temp.seqmat[1, i-3]
+                    print(index / 3, codon)
                     return SeqMat().set_seqmat(temp.subseq_prefix(index))  # Not include the stop codon
 
             # If no stop codon is found, return the full sequence

{geney-1.2.25.dist-info → geney-1.2.27.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.25
+Version: 1.2.27
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.25.dist-info → geney-1.2.27.dist-info}/RECORD

@@ -9,7 +9,7 @@ geney/mutation_utils.py,sha256=C-K8F8wyN5joI3ZuP-d7IMYTI43YPDXUc3IgAJ07o8Q,1546
 geney/oncosplice.py,sha256=3jJc1-CWubH2ElHEjyQtsr9JYVmfPQEpq7EX-IfY-t8,20806
 geney/pangolin_utils.py,sha256=S2uMjQnnxqWSnfuMaEjo-wq52DVKFiXt__L5VPdtzyU,2939
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=JZk-dY7SjHESK1NaXfWuDpZGLJkeT_03ZfZS6gHBEr0,16796
+geney/seqmat_utils.py,sha256=nqz5Ovj3IIb16YMrwqYd9EIWzLUA2qpGTkycZYVIqdY,16848
 geney/spliceai_utils.py,sha256=gIGPC8u3J15A7EQrk2Elho5PbF9MmUUNopGGH-eEV8s,1873
 geney/splicing_utils.py,sha256=pS3jZEpmnDkbT1jjaJh-O6I--Xm22e5dj-GQu7IAZSQ,15943
 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-1.2.25.dist-info/METADATA,sha256=RUiiqgqgJ0Qr9_iJvEds3xzIrFhPiW9qd-DBkdb2SxI,948
-geney-1.2.25.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.25.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.25.dist-info/RECORD,,
+geney-1.2.27.dist-info/METADATA,sha256=9xI__6EWbE9WIxf0V_JCYGGqC5dPgujwQ6cLUMrmHrU,948
+geney-1.2.27.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.27.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.27.dist-info/RECORD,,