geney 1.2.62__py2.py3-none-any.whl → 1.2.63__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -145,6 +145,17 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
     return discovered_pos, deleted_pos
 
 
+def find_transcript_missplicing_mutid(mut_id):
+    from geney.seqmat_utils import Gene
+    transcript = Gene(mut_id.split(':')[0]).transcript().generate_mature_mrna()
+    out = find_transcript_missplicing(transcript, [get_mutation(mut_id, rev=transcript.rev)], context=5000, window=2500, threshold=0.5, engine='spliceai', just_ss=True)
+    best_delta = 0
+    for k, v in out.items():
+        for k1, v1 in v.items():
+            if abs(v1['delta']) > abs(best_delta):
+                best_delta = v1['delta']
+    return best_delta
+
 def find_transcript_missplicing(transcript, mutations, context=5000, window=2500, threshold=0.5, engine='spliceai', just_ss=False):
     from functools import reduce
     ref = transcript.pre_mrna

{geney-1.2.62.dist-info → geney-1.2.63.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.62
+Version: 1.2.63
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.62.dist-info → geney-1.2.63.dist-info}/RECORD

@@ -11,7 +11,7 @@ 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/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=YwUafW97W0_87DcFINgSEPI3pRfpbcbBahKNUAb-phE,18299
+geney/splicing_utils.py,sha256=nYfdM-ppHS1kUrwzDcS6VHxpHGv3vVl4p7f_JWKZTL8,18831
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -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-1.2.62.dist-info/METADATA,sha256=AW_GSC1eYornvODYRHbZ5_z7BdXLACAfOehKpa-FyWA,948
-geney-1.2.62.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.62.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.62.dist-info/RECORD,,
+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,,