geney 1.3.24__py2.py3-none-any.whl → 1.3.25__py2.py3-none-any.whl

geney/SeqMats.py

@@ -453,6 +453,9 @@ class MutSeqMat(SeqMat):
         if not (np.all(abs(np.diff(indices)) <= 1)):
             raise ValueError(f"Mutation indices must be consecutive. Got: {indices}")
 
+    @property
+    def indices(self):
+        return self.seqmat[self.ROW_INDS, :] + (self.seqmat[self.ROW_SUPERINDS, :] / 10)
 
     @classmethod
     def from_mutid(cls, mid):

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] for m in mutations]) // 1 - 1
+    center = np.mean([m.indices[0] - 2 for m in mutations]) // 11
     for mutation in mutations:
         variant_transcript.mutate(mutation, inplace=True)
 

{geney-1.3.24.dist-info → geney-1.3.25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.24
+Version: 1.3.25
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.24.dist-info → geney-1.3.25.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=-Wx9fCSTZL98UoTKZGj6fKDnT4zsJHFuvuHabSoXTU0,18712
+geney/SeqMats.py,sha256=0wL3mLeNhLOqNYioMTV02zN8dnER67JwD6wkNxp44mU,18838
 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=T5pV9DwVCa1ApoHUVLENAK8-EipYowb2zIdutikww_s,35567
+geney/splicing_utils.py,sha256=s6jns493Fh1xwyxIT1sYdd5_VyIZdeK27rupS1kG_LI,35568
 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-1.3.24.dist-info/METADATA,sha256=QGMCWLfATo68aqlgfFEARrEnv0bQA_qu6kJIORLFC5Q,971
-geney-1.3.24.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.24.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.24.dist-info/RECORD,,
+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,,