geney 1.3.77__py2.py3-none-any.whl → 1.3.79__py2.py3-none-any.whl

geney/Transcript.py

@@ -367,7 +367,7 @@ class Transcript:
             Transcript or (protein: str, cons_vector: np.ndarray): The Transcript object if inplace=True, else the protein and cons_vector.
         """
         if not self.protein_coding:
-            print("No protein can be generated without TIS/TTS.")
+            # print("No protein can be generated without TIS/TTS.")
             return self if inplace else ("", np.array([]))
 
         # Translate the ORF to protein

geney/oncosplice.py

@@ -286,7 +286,7 @@ def summarize_missplicing_event(pes, pir, es, ne, ir):
 def missense_effect(r, v):
     nt_changes, aa_changes = '', ''
     if len(r.protein) != len(v.protein) or len(r.orf) != len(v.orf):
-        return '', '', -1
+        return '', ''
 
     if r.protein != v.protein:
         for i, (x, y) in enumerate(zip(r.protein, v.protein)):
@@ -318,10 +318,9 @@ def OncospliceAnnotator(reference_transcript, variant_transcript, mut, ref_attri
     report['affected_intron'] = affected_intron
     report['mutation_distance_from_5'] = distance_from_5
     report['mutation_distance_from_3'] = distance_from_3
-    aa_c, c_c, pos = missense_effect(reference_transcript, variant_transcript)
+    aa_c, c_c = missense_effect(reference_transcript, variant_transcript)
     report['missense_effect'] = aa_c
     report['codon_change'] = c_c
-    report['missense_position'] = pos
     return report
 
 

geney/spliceai_utils.py

@@ -6,10 +6,10 @@ import tensorflow as tf
 import sys
 
 # Check if GPU is available
-if tf.config.list_physical_devices('GPU'):
-    print("Running on GPU.")
-else:
-    print("Running on CPU.")
+# if tf.config.list_physical_devices('GPU'):
+#     print("Running on GPU.")
+# else:
+#     print("Running on CPU.")
 
 # tf.config.threading.set_intra_op_parallelism_threads(1)
 # tf.config.threading.set_inter_op_parallelism_threads(1)
@@ -18,21 +18,21 @@ else:
 model_filenames = [f"models/spliceai{i}.h5" for i in range(1, 6)]
 
 # Load each model using the package resources.
-sai_models = [load_model(resources.files("spliceai").joinpath(filename))
-              for filename in model_filenames]
+# sai_models = [load_model(resources.files("spliceai").joinpath(filename))
+#               for filename in model_filenames]
 
-# if sys.platform == 'darwin':
-#     sai_paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))
-#     # sai_models = [load_model(resource_filename('spliceai', x)) for x in sai_paths]
-#     sai_models = [load_model(resources.files('spliceai').joinpath(f)) for f in sai_paths]
-# else:
-#     sai_paths = ['/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai1.h5',
-#                  '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai2.h5',
-#                  '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai3.h5',
-#                  '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai4.h5',
-#                  '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai5.h5']
+if sys.platform == 'darwin':
+    sai_paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))
+    # sai_models = [load_model(resource_filename('spliceai', x)) for x in sai_paths]
+    sai_models = [load_model(resources.files('spliceai').joinpath(f)) for f in sai_paths]
+else:
+    sai_paths = ['/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai1.h5',
+                 '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai2.h5',
+                 '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai3.h5',
+                 '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai4.h5',
+                 '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai5.h5']
 
-    # sai_models = [load_model(f) for f in sai_paths]
+    sai_models = [load_model(f) for f in sai_paths]
 
 
 def one_hot_encode(seq):

{geney-1.3.77.dist-info → geney-1.3.79.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.77
+Version: 1.3.79
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.77.dist-info → geney-1.3.79.dist-info}/RECORD

@@ -1,7 +1,7 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
 geney/Gene.py,sha256=2eznhavDoO4rktisy3U0uz480OsktppEwH5pxC2qoog,7083
 geney/SeqMats.py,sha256=9-eJnfU2w3LGc0XvVvFEO_QrBneTkC6xkZKDfTcEw5o,19282
-geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
+geney/Transcript.py,sha256=xI611PUr311cVgvzhXFoK8nXlFRnaZ8qbdGabTUY9hE,14501
 geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
 geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
 geney/allele_linkage.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -11,11 +11,11 @@ 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=hADoNLoIt_f6O2lnFL0YpIOam3mOBy0BLJUNzV4npoc,32355
+geney/oncosplice.py,sha256=7KpuvIMLEZ4VGPIOw-UUwiPGfQgeFVrapqNt6jLreRA,32308
 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=V5DccGjm2GZQINSVxJYPoN8iYQzU4gE9tINy6gmHjOM,3304
+geney/spliceai_utils.py,sha256=nyBnLdYs1rB-duA9lfJYM9Q2xNlvZA3I_sCJ1z5WjFw,3294
 geney/splicing_utils.py,sha256=UkG2YphjLNUYsv3o3RGUTW1ScHbEMOLL2M_7WbgDVME,47466
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=uJhVnTbTysj0XrEw_YeDKRSLexsqgBLYQdhl7_hnr64,17611
@@ -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-1.3.77.dist-info/METADATA,sha256=7eMKlyiIIgYM794hncNt_lj1fyK6KzWc5zbTb8O4bw0,990
-geney-1.3.77.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.77.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.77.dist-info/RECORD,,
+geney-1.3.79.dist-info/METADATA,sha256=4vRmkHDHpg91Ci8mbzJHfrvx0xxpeXs_jL7YBXYhDjU,990
+geney-1.3.79.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.79.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.79.dist-info/RECORD,,