geney 1.3.54__py2.py3-none-any.whl → 1.3.56__py2.py3-none-any.whl

geney/oncosplice.py

@@ -319,14 +319,15 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
 
     results = []
     for reference_transcript in tqdm(gene, desc=f'Processing {mut_id}...'):
-        if (cons_required and not reference_transcript.cons_available) or (
-                protein_coding and not reference_transcript.transcript_biotype == 'protein_coding'):
-            print("Missing either protein coding or conservation...")
+        # if (cons_required and not reference_transcript.cons_available) or (
+        #         protein_coding and not reference_transcript.transcript_biotype == 'protein_coding'):
+        if protein_coding and not reference_transcript.transcript_biotype == 'protein_coding':
+            print("Not protein coding...")
             continue
 
         current_mutations = [m for m in mutations if m in reference_transcript]
         if len(current_mutations) == 0:
-            print("No mutations within transcript...")
+            print(f"No mutations within transcript ({reference_transcript.transcript_start} > {reference_transcript.transcript_end})...")
             continue
 
         center = np.mean([m.indices[0] for m in current_mutations]) // 1
@@ -337,7 +338,8 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
             mutated_transcript.mutate(mutation, inplace=True)
 
         reference_transcript.generate_mature_mrna().generate_protein()
-        if '*' in reference_transcript.protein or len(reference_transcript.protein) < window_length:
+        # if ('*' in reference_transcript.protein or
+        if len(reference_transcript.protein) < window_length:
             print(f"> Errors in reference transcript {reference_transcript.transcript_id}")
             continue
 

{geney-1.3.54.dist-info → geney-1.3.56.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.54
+Version: 1.3.56
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.54.dist-info → geney-1.3.56.dist-info}/RECORD

@@ -11,7 +11,7 @@ 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=ghEY6HEJKpQrJYT26sVbXpTuqMrR4YmMV7JuAL4a8jQ,24424
+geney/oncosplice.py,sha256=S4zitixt8pwxFCLJlOC6XAx5e8EVdUEyXoO2ZssLAaw,24593
 geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
@@ -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-1.3.54.dist-info/METADATA,sha256=LsSWWFwaNOC6ZybBz-WtvRe52StF82EzNHe3zjYg63Q,990
-geney-1.3.54.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.54.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.54.dist-info/RECORD,,
+geney-1.3.56.dist-info/METADATA,sha256=ywk8WyoHHwiZUG8VbDcKGxUxNmPpKrufrPA8n1xgq6g,990
+geney-1.3.56.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.56.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.56.dist-info/RECORD,,