geney 1.3.11__py2.py3-none-any.whl → 1.3.13__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -137,10 +137,10 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
                 list(set(list(ref_dct.keys()) + list(mut_dct.keys())))}
 
     discovered_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct[k]), 3), 'reference': round(ref_dct[k], 3)} for k, v in
-                      new_dict.items() if v >= threshold} # and k not in known_splice_sites}   # if (k not in known_splice_sites and v >= threshold) or (v > 0.45)}
+                      new_dict.items() if v >= threshold and k not in known_splice_sites}   # if (k not in known_splice_sites and v >= threshold) or (v > 0.45)}
 
     deleted_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct.get(k, 0)), 3), 'reference': round(ref_dct[k], 3)} for k, v in
-                   new_dict.items() if -v >= threshold} # and k in known_splice_sites}      #if k in known_splice_sites and v <= -threshold}
+                   new_dict.items() if -v >= threshold and k in known_splice_sites}      #if k in known_splice_sites and v <= -threshold}
 
     return discovered_pos, deleted_pos
 
@@ -356,9 +356,13 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False):
     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 = 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(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)
 
         if fprint:
             print(missplicing1)
@@ -411,7 +415,7 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False):
                     flag['cummulative'] += 1
                     cummulative_deltas.append(max((deltab - delta1, deltab - delta2), key=abs))
 
-                if ((0.25 <= ref_val) <= 0.75) and (
+                if ((0.4 <= ref_val) <= 0.75) and (
                         ((delta1 > 0.25 or delta2 > 0.25) and deltab < 0.25) or
                         (delta1 < 0.25 and delta2 < 0.25 and deltab > 0.25)
                 ) and (
@@ -457,8 +461,9 @@ class Missplicing:
         self.threshold = threshold
 
     def __str__(self):
+        import pprint
         """String representation displays the filtered splicing events passing the threshold."""
-        return str(self.significant_events)
+        return pprint.pprint(self.aberrant_splicing)
 
     def __bool__(self):
         """
@@ -528,6 +533,7 @@ class Missplicing:
             return splicing_dict
         return None
 
+    @property
     def max_delta(self):
         """
         Returns the maximum absolute delta found in all events.

{geney-1.3.11.dist-info → geney-1.3.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.11
+Version: 1.3.13
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.11.dist-info → geney-1.3.13.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=Bj5YV-LHs684afjriep7N2QaRAAKdidFS-adihfDzfI,31887
+geney/splicing_utils.py,sha256=mBZGTF57BZ3caTnkQ_8zMhv7z0iRPrGKBSmjeDnTiUc,32222
 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-1.3.11.dist-info/METADATA,sha256=Por9VSaGxOGXy61knApS-3BefXSrh8hhQQQ0ULGQn2I,971
-geney-1.3.11.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.11.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.11.dist-info/RECORD,,
+geney-1.3.13.dist-info/METADATA,sha256=yi0VHNzHaCHWqKRpAMHtF4tgWICSO0uYi1TJMDq5BIw,971
+geney-1.3.13.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.13.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.13.dist-info/RECORD,,