geney 1.3.18__py2.py3-none-any.whl → 1.3.20__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -363,22 +363,20 @@ def find_transcript_missplicing_seqs(ref_seq, var_seq, donors, acceptors, thresh
     missplicing = {'missed_acceptors': dap, 'missed_donors': ddp, 'discovered_acceptors': iap,
                    'discovered_donors': idp}
     missplicing = {outk: {float(k): v for k, v in outv.items()} for outk, outv in missplicing.items()}
-    temp = {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in
+    missplicing = {outk: {int(k) if k.is_integer() else k: v for k, v in outv.items()} for outk, outv in
             missplicing.items()}
-    return Missplicing(temp, threshold=threshold)
+    print(missplicing)
+    return Missplicing(missplicing, threshold=threshold)
 
 
 def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
     results = []
     for mid in mids:
         m1, m2 = mid.split('|')
-        # missplicing1 = find_transcript_missplicing(m1, threshold=0.25, engine=engine)
-        # missplicing2 = find_transcript_missplicing(m2, threshold=0.25, engine=engine)
-        # missplicing_both = find_transcript_missplicing(mid, threshold=0.25, engine=engine)
 
-        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)
+        missplicing1 = find_transcript_missplicing(m1, engine=engine, db=db)
+        missplicing2 = find_transcript_missplicing(m2, engine=engine, db=db)
+        missplicing_both = find_transcript_missplicing(mid, engine=engine, db=db)
 
         if fprint:
             print(missplicing1)
@@ -444,9 +442,9 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
 
         vals = cummulative_deltas + corrective_deltas
         flag['max_delta'] = max(vals, key=abs) if vals else 0
-        flag['ms1'] = missplicing1.max_delta()
-        flag['ms2'] = missplicing2.max_delta()
-        flag['msb'] = missplicing_both.max_delta()
+        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
@@ -551,6 +549,7 @@ class Missplicing:
             return splicing_dict
         return None
 
+    @property
     def max_delta(self):
         """
         Returns the maximum absolute delta found in all events.
@@ -558,8 +557,10 @@ class Missplicing:
         Returns:
             float: The maximum absolute delta, or 0 if no events.
         """
-        deltas = [detail['delta'] for details in self.missplicing.values() for detail in details.values()]
-        return max(deltas, key=abs, default=0.0)
+        max_deltas = []
+        for k, v in self.missplicing.items():
+            max_deltas.extend([sv['delta'] for sv in v.values()])
+        return max(max_deltas, key=abs, default=0.0)
 
 
 # def find_transcript_splicing(transcript, engine='spliceai'):

{geney-1.3.18.dist-info → geney-1.3.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.18
+Version: 1.3.20
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.18.dist-info → geney-1.3.20.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=EI1FzSsmyRSuBn-kByWme8pNM5ANvixSDv12aI4aVJA,35839
+geney/splicing_utils.py,sha256=Kke4Lc8MKR0ZjTzFnvO_NyIzXxDzoqYsJTo0ZHES4ZQ,35561
 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-1.3.18.dist-info/METADATA,sha256=uQn76W27wqF8-VmiuVWrHEgursCrihW_dlQhg4X4Wgk,971
-geney-1.3.18.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.18.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.18.dist-info/RECORD,,
+geney-1.3.20.dist-info/METADATA,sha256=qDlw9g8vl1u8Ww6_HGEw3dc2XAVARwY4gwODLNvTDvQ,971
+geney-1.3.20.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.20.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.20.dist-info/RECORD,,