geney 1.3.47__py2.py3-none-any.whl → 1.3.49__py2.py3-none-any.whl

geney/oncosplice.py

@@ -321,10 +321,12 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
     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...")
             continue
 
         current_mutations = [m for m in mutations if m in reference_transcript]
         if len(current_mutations) == 0:
+            print("No mutations within transcript...")
             continue
 
         center = np.mean([m.indices[0] for m in current_mutations]) // 1

geney/pangolin_utils.py

@@ -15,6 +15,7 @@ if sys.platform == 'darwin':
 if sys.platform == 'linux':
     device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu")
 
+print(f"Pangolin loaded to {device}.")
 
 for i in pang_model_nums:
     for j in range(1, 6):

geney/splicing_utils.py

@@ -145,10 +145,10 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
     new_dict = {v: mut_dct.get(v, 0) - ref_dct.get(v, 0) for v in
                 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
+    discovered_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct[k]), 3), 'reference': round(ref_dct.get(k, 0), 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)}
 
-    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
+    deleted_pos = {k: {'delta': round(float(v), 3), 'absolute': round(float(mut_dct.get(k, 0)), 3), 'reference': round(ref_dct.get(k, 0), 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}
 
     return discovered_pos, deleted_pos

{geney-1.3.47.dist-info → geney-1.3.49.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.47
+Version: 1.3.49
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.47.dist-info → geney-1.3.49.dist-info}/RECORD

@@ -11,12 +11,12 @@ 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=q1W8k4nvRzQPH7LZsefTky6Nw2Kmx-DDXZ_UCty0Wog,24299
-geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
+geney/oncosplice.py,sha256=ghEY6HEJKpQrJYT26sVbXpTuqMrR4YmMV7JuAL4a8jQ,24424
+geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 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=WflxRPfc4DzeHuYOZqjpa-YD1nuZzs7h_WCsv-LX87A,38498
+geney/splicing_utils.py,sha256=GDSuuy8kWBh2_4UDwqjclF9gKnnCoLc_neOEsSrNWQM,38512
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
@@ -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-1.3.47.dist-info/METADATA,sha256=EuYNvrU5I5CM9PfqnNd3Yk_lo3VxNn97eCFaPIyO4rE,990
-geney-1.3.47.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.47.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.47.dist-info/RECORD,,
+geney-1.3.49.dist-info/METADATA,sha256=1tglGOcOnNBzE0M3lN2mo_J26uWPPNYFN_pNHVHHQiA,990
+geney-1.3.49.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.49.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.49.dist-info/RECORD,,