geney 1.3.15__py2.py3-none-any.whl → 1.3.17__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -230,7 +230,7 @@ def find_transcript_missplicing(mut_id, transcript=None, threshold=0.5, engine='
     for mutation in mutations:
         variant_transcript.mutate(mutation, inplace=True)
 
-    missplicing = find_transcript_missplicing_seqs(reference_transcript.pre_mrna.get_context(center, 7500), variant_transcript.pre_mrna.get_context(center, 7500), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
+    missplicing = find_transcript_missplicing_seqs(reference_transcript.pre_mrna.get_context(center, 7500, padding='N'), variant_transcript.pre_mrna.get_context(center, 7500, padding='N'), reference_transcript.donors, reference_transcript.acceptors, threshold=threshold, engine=engine)
 
     if db is not None:
         db.store_mutation_data(engine, gene.gene_name, mut_id, reference_transcript.transcript_id, missplicing.missplicing)
@@ -368,7 +368,7 @@ def find_transcript_missplicing_seqs(ref_seq, var_seq, donors, acceptors, thresh
     return Missplicing(temp, threshold=threshold)
 
 
-def process_pairwise_epistasis(mids, engine='pangolin', fprint=False):
+def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
     results = []
     for mid in mids:
         m1, m2 = mid.split('|')
@@ -376,9 +376,9 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False):
         # missplicing2 = find_transcript_missplicing(m2, threshold=0.25, engine=engine)
         # missplicing_both = find_transcript_missplicing(mid, threshold=0.25, engine=engine)
 
-        missplicing1 = Missplicing(get_or_compute_splicing(m1, engine=engine), threshold=0.25)
-        missplicing2 = Missplicing(get_or_compute_splicing(m2, engine=engine), threshold=0.25)
-        missplicing_both = Missplicing(get_or_compute_splicing(mid, engine=engine), threshold=0.25)
+        missplicing1 = Missplicing(find_transcript_missplicing(m1, engine=engine, db=db), threshold=0.25)
+        missplicing2 = Missplicing(find_transcript_missplicing(m2, engine=engine, db=db), threshold=0.25)
+        missplicing_both = Missplicing(find_transcript_missplicing(mid, engine=engine, db=db), threshold=0.25)
 
         if fprint:
             print(missplicing1)
@@ -444,9 +444,9 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False):
 
         vals = cummulative_deltas + corrective_deltas
         flag['max_delta'] = max(vals, key=abs) if vals else 0
-        flag['ms1'] = max(ms1, key=abs)
-        flag['ms2'] = max(ms2, key=abs)
-        flag['msb'] = max(msb, key=abs)
+        flag['ms1'] = missplicing1.max_delta
+        flag['ms2'] = missplicing2.max_delta
+        flag['msb'] = missplicing_both.max_delta
         flag['increased_canonical_splicing'] = increased_canonical_splicing
 
         result_df = pd.Series(flag).to_frame().T

{geney-1.3.15.dist-info → geney-1.3.17.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.15
+Version: 1.3.17
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.15.dist-info → geney-1.3.17.dist-info}/RECORD

@@ -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=shRi6eaIrXg6ZfnTEIVMb7Cl51a1E3swpXH-qz0whKo,35760
+geney/splicing_utils.py,sha256=T1aNSRwhyJdYU4_FrkHnUEqtXSs8NuvTqjpGMAGIgCk,35847
 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-1.3.15.dist-info/METADATA,sha256=QUp06fi0VTP_o0jI2M9v65lQq8rRzYIN9XRtefazSOA,971
-geney-1.3.15.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.15.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.15.dist-info/RECORD,,
+geney-1.3.17.dist-info/METADATA,sha256=djgaQGPdsWph1mXqld_kAD5O6awvDoMFSHxqIm0rXiM,971
+geney-1.3.17.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.17.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.17.dist-info/RECORD,,