geney 1.2.60__py2.py3-none-any.whl → 1.2.62__py2.py3-none-any.whl

geney/pangolin_utils.py

@@ -5,7 +5,7 @@ from pangolin.model import *
 import numpy as np
 import sys
 
-pang_model_nums = [0, 1, 2, 3, 4, 5, 6]
+pang_model_nums = [0, 1, 2, 3, 4, 5, 6, 7]
 pang_models = []
 
 device = torch.device('cpu')

geney/seqmat_utils.py

@@ -241,6 +241,14 @@ class Gene:
         key = list(self.transcripts.keys())[index]
         return Transcript(self.transcripts[key])
 
+    def splice_sites(self):
+        from collections import Counter
+        acceptors, donors = [], []
+        for transcript in self.transcripts.values():
+            acceptors.extend(transcript['acceptors'])
+            donors.extend(transcript['donors'])
+        return Counter(acceptors), Counter(donors)
+
     def transcript(self, tid=None):
         if tid is None:
             tid = self.primary_transcript

geney/splicing_utils.py

@@ -173,8 +173,6 @@ def find_transcript_missplicing(transcript, mutations, context=5000, window=2500
     ref_seq = 'N'*ref_start_pad + ref.seq + 'N'*ref_end_pad
     var_seq = 'N'*var_start_pad + var.seq + 'N'*var_end_pad
 
-    # print(ref_seq)
-
     if engine == 'spliceai':
         from .spliceai_utils import sai_predict_probs, sai_models
         ref_seq_acceptor_probs, ref_seq_donor_probs = sai_predict_probs(ref_seq, models=sai_models)

{geney-1.2.60.dist-info → geney-1.2.62.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.60
+Version: 1.2.62
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.60.dist-info → geney-1.2.62.dist-info}/RECORD

@@ -7,11 +7,11 @@ geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
 geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
 geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
 geney/oncosplice.py,sha256=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
-geney/pangolin_utils.py,sha256=Hsq9Y_GLFHGqEDn25_VdD7YKUYxpjMlynj0z-B_LezE,2931
+geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=hIikPuybVdZ3ZU9WlaTs6ON7U0AVQv5Kya4CXhKIt-s,18351
+geney/seqmat_utils.py,sha256=f-4dtufdKHc52jf_xZqbwBu-DXCa2Tl0Wsigguus6-E,18661
 geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
-geney/splicing_utils.py,sha256=I_YKc5O0djYY5VgDqBb0JFYogPEUyH6n9B_IngAw33Y,18321
+geney/splicing_utils.py,sha256=YwUafW97W0_87DcFINgSEPI3pRfpbcbBahKNUAb-phE,18299
 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-1.2.60.dist-info/METADATA,sha256=hot8OpcKUrw3KWJcUS8NtgHvggVmM9CSNteWAinAVls,948
-geney-1.2.60.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.60.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.60.dist-info/RECORD,,
+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,,