geney 1.3.62__py2.py3-none-any.whl → 1.3.64__py2.py3-none-any.whl

geney/oncosplice.py

@@ -368,9 +368,10 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
                 if no_splicing_record and splicing_db is not None:
                     splicing_db.store_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene.gene_name, transcript_id=reference_transcript.transcript_id, data=missplicing.missplicing)
 
-        alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing.missplicing)
-        print("iterating through new boundaries...")
+        alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing) #.missplicing)
         for i, new_boundaries in enumerate(alternative_splicing_paths):
+            print("iterating through new boundaries...")
+
             mutated_transcript.acceptors = new_boundaries['acceptors']
             mutated_transcript.donors = new_boundaries['donors']
             mutated_transcript.generate_mature_mrna().generate_protein()

geney/splicing_utils.py

@@ -1,5 +1,7 @@
 import numpy as np
 import pandas as pd
+from tensorflow.python.framework.test_ops import none_eager_fallback
+
 from .Gene import Gene
 from .SeqMats import MutSeqMat
 from collections import defaultdict
@@ -119,15 +121,19 @@ def prepare_splice_sites(acceptors, donors, aberrant_splicing):
 
 
 def develop_aberrant_splicing(transcript, aberrant_splicing):
-    all_acceptors, all_donors = prepare_splice_sites(transcript.acceptors, transcript.donors, aberrant_splicing)
-    adj_list = generate_adjacency_list(all_acceptors, all_donors, transcript_start=transcript.transcript_start,
-                                       transcript_end=transcript.transcript_end, rev=transcript.rev,
-                                       max_distance=100000)
-    end_node = (transcript.transcript_end, 'transcript_end')
-    start_node = (transcript.transcript_start, 'transcript_start')
-    for path, prob in find_all_paths(adj_list, start_node, end_node):
-        yield {'acceptors': [p[0] for p in path if p[1] == 'acceptor'],
-               'donors': [p[0] for p in path if p[1] == 'donor'], 'path_weight': prob}
+    if not aberrant_splicing:
+        yield {'acceptors': transcript.acceptors, 'donors': transcript.donors, 'path_weight': 1}
+
+    else:
+        all_acceptors, all_donors = prepare_splice_sites(transcript.acceptors, transcript.donors, aberrant_splicing.missplicing)
+        adj_list = generate_adjacency_list(all_acceptors, all_donors, transcript_start=transcript.transcript_start,
+                                           transcript_end=transcript.transcript_end, rev=transcript.rev,
+                                           max_distance=100000)
+        end_node = (transcript.transcript_end, 'transcript_end')
+        start_node = (transcript.transcript_start, 'transcript_start')
+        for path, prob in find_all_paths(adj_list, start_node, end_node):
+            yield {'acceptors': [p[0] for p in path if p[1] == 'acceptor'],
+                   'donors': [p[0] for p in path if p[1] == 'donor'], 'path_weight': prob}
 
 
 

{geney-1.3.62.dist-info → geney-1.3.64.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.62
+Version: 1.3.64
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.62.dist-info → geney-1.3.64.dist-info}/RECORD

@@ -11,12 +11,12 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
 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=YyoJEBY8yKsaKGFXmH_nJRfzb6gBfuMq9lV89H3A9D0,24785
+geney/oncosplice.py,sha256=YZvAnbe8gj9fPvs2DldeQpqhhe_QR9xBLe_0tcm9tdg,24793
 geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 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=GDSuuy8kWBh2_4UDwqjclF9gKnnCoLc_neOEsSrNWQM,38512
+geney/splicing_utils.py,sha256=cVLXArVWJIxGaaWttm_dxJQbo6OBBkry4OFozaw-M2U,38768
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
@@ -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-1.3.62.dist-info/METADATA,sha256=JaEKHBPqwIUagmuVLomjmNJhs0vF_pT3bK6z7gsPGRc,990
-geney-1.3.62.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.62.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.62.dist-info/RECORD,,
+geney-1.3.64.dist-info/METADATA,sha256=UBUHpebp0LZs-uSCEwFF0snqM-FoUX8mC2-1HaBx3cY,990
+geney-1.3.64.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.64.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.64.dist-info/RECORD,,