geney 1.3.28__py2.py3-none-any.whl → 1.3.30__py2.py3-none-any.whl

geney/Gene.py

@@ -138,6 +138,9 @@ class Gene:
         if tid is None:
             tid = self.primary_transcript
 
+        if tid is None:
+            return Transcript()
+
         if tid not in self.transcripts:
             raise AttributeError(f"Transcript '{tid}' not found in gene '{self.gene_name}'.")
 
@@ -170,6 +173,12 @@ class Gene:
             self._primary_transcript = protein_coding[0]
             return self._primary_transcript
 
+        # # Fallback 2: find a proitein coding transcript that is not fully defined
+        # protein_coding = [k for k, v in self.transcripts.items() if v.get('transcript_biotype') == 'protein_coding_CDS_not_defined']
+        # if protein_coding:
+        #     self._primary_transcript = protein_coding[0]
+        #     return self._primary_transcript
+
         # No primary or protein-coding transcript found
         self._primary_transcript = None
         return None

geney/splicing_utils.py

@@ -385,7 +385,7 @@ def process_pairwise_epistasis(mids, engine='pangolin', fprint=False, db=None):
             print(missplicing_both)
 
         max_delta = 0
-        flag = {'mut_id': mid, 'corrective': 0, 'cummulative': 0}
+        flag = {'mut_id': mid, 'corrective': 0, 'cumulative': 0}
         cummulative_deltas, corrective_deltas = [], []
         ms1, ms2, msb = [], [], []
         increased_canonical_splicing = False

{geney-1.3.28.dist-info → geney-1.3.30.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.28
+Version: 1.3.30
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.28.dist-info → geney-1.3.30.dist-info}/RECORD

@@ -1,5 +1,5 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
-geney/Gene.py,sha256=JGWtfA6-d1W3I9YRASwaF8vaZ6CCuY0KEawQNdloIqY,6259
+geney/Gene.py,sha256=1pqKI3hGZndi7VY4j66ObhJjnz8YiNtBLGJTIHWVujA,6670
 geney/SeqMats.py,sha256=aLpqd7RJSEU07jdPXpbtZPeb2D9BxrZuW6BTkcXpNE4,18819
 geney/Transcript.py,sha256=eRZXVVxDVBbv0l385bnAOBFRBSzBwppXcbBq8KXkwlo,14443
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
@@ -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=5XJH5hIhuiD-u2EKKz0pr98hSv5i2mFAnUj83jHHZRc,38486
+geney/splicing_utils.py,sha256=elu5KtkcNGTWhviimIRt0DRWNcjwZrshDphM5XFPImA,38485
 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-1.3.28.dist-info/METADATA,sha256=doHL3Z_Xz-ygh80f98ZZBsBr2Hr1hm8C1n8-OWE08ls,990
-geney-1.3.28.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.28.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.28.dist-info/RECORD,,
+geney-1.3.30.dist-info/METADATA,sha256=ZS6Ft5TJYV5WFTOM47ny7m7eSA76C2EmCEMD2yuBhcQ,990
+geney-1.3.30.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.30.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.30.dist-info/RECORD,,