geney 1.3.25__py2.py3-none-any.whl → 1.3.26__py2.py3-none-any.whl

geney/SeqMats.py

@@ -213,8 +213,9 @@ class SeqMat:
 
 
     def _rel_index(self, pos):
-        pos = int(pos)
-        if pos in self.indices:
+        # pos = int(pos)
+        print("sup")
+        if pos in self.raw_indices:
             return np.where(self.seqmat[self.ROW_INDS, :] == pos)[0][0]
         else:
             raise IndexError(f"Position {pos} not found in sequence.")

geney/splicing_utils.py

@@ -226,7 +226,7 @@ def find_transcript_missplicing(mut_id, transcript=None, threshold=0.5, engine='
     if len(mutations) == 0:
         return Missplicing({'missed_acceptors': {}, 'missed_donors': {}, 'discovered_acceptors': {}, 'discovered_donors': {}})
 
-    center = np.mean([m.indices[0] - 2 for m in mutations]) // 11
+    center = np.mean([m.indices[0] for m in mutations]) // 11
     for mutation in mutations:
         variant_transcript.mutate(mutation, inplace=True)
 

{geney-1.3.25.dist-info → geney-1.3.26.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.25
+Version: 1.3.26
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn
@@ -19,9 +19,9 @@ Requires-Dist: networkx
 Requires-Dist: viennarna
 Requires-Dist: tqdm
 Requires-Dist: spliceai
-Requires-Dist: biopython ==1.81
-Requires-Dist: gtfparse ==1.3.0
-Requires-Dist: sh ==2.0.6
+Requires-Dist: biopython==1.81
+Requires-Dist: gtfparse==1.3.0
+Requires-Dist: sh==2.0.6
 Requires-Dist: torch
 Requires-Dist: lifelines
 Requires-Dist: notebook

{geney-1.3.25.dist-info → geney-1.3.26.dist-info}/RECORD

@@ -1,6 +1,6 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
 geney/Gene.py,sha256=JGWtfA6-d1W3I9YRASwaF8vaZ6CCuY0KEawQNdloIqY,6259
-geney/SeqMats.py,sha256=0wL3mLeNhLOqNYioMTV02zN8dnER67JwD6wkNxp44mU,18838
+geney/SeqMats.py,sha256=jC_0MnvJxKNb7_L-fgEWMd8Wi-4KVuvDbMCSFSqfL7w,18865
 geney/Transcript.py,sha256=eRZXVVxDVBbv0l385bnAOBFRBSzBwppXcbBq8KXkwlo,14443
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
 geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
@@ -16,7 +16,7 @@ geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=s6jns493Fh1xwyxIT1sYdd5_VyIZdeK27rupS1kG_LI,35568
+geney/splicing_utils.py,sha256=nsOCSjknIjbPUwAVWyig1q9OrQ-Q21dgkgmbzpvL0G4,35564
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -25,7 +25,7 @@ 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-1.3.25.dist-info/METADATA,sha256=6471Hndd8IYKiZcRx_VynahCihRDdhnkgu4IJZ8KU-g,971
-geney-1.3.25.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.25.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.25.dist-info/RECORD,,
+geney-1.3.26.dist-info/METADATA,sha256=mTYsp6ghf5TMklnrKNBIUZ6-JBX1_CYZXnF-RKBMPaQ,968
+geney-1.3.26.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.26.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.26.dist-info/RECORD,,