geney 1.4.4__py2.py3-none-any.whl → 1.4.6__py2.py3-none-any.whl

geney/Gene.py

@@ -3,7 +3,7 @@ import copy
 from . import config
 from typing import Any, Dict, List, Tuple, Optional, Iterator, Union, TYPE_CHECKING
 from collections import Counter
-from .utils import unload_pickle
+from .utils.utils import unload_pickle
 from .Transcript import Transcript
 
 class Gene:

geney/utils/__init__.py

@@ -7,14 +7,14 @@ __all__ = []  # This will collect all the names you want to expose
 # Find all utility modules in this directory
 _package_dir = pathlib.Path(__file__).parent
 
-for file in os.listdir(_package_dir):
-    if file.endswith(".py") and file != "__init__.py":
-        module_name = file[:-3]  # strip '.py'
-        module_path = f"{__name__}.{module_name}"
-        module = importlib.import_module(module_path)
-
-        # If the module defines __all__, expose those names at utils level
-        if hasattr(module, "__all__"):
-            for name in module.__all__:
-                globals()[name] = getattr(module, name)
-                __all__.append(name)
+# for file in os.listdir(_package_dir):
+#     if file.endswith(".py") and file != "__init__.py":
+#         module_name = file[:-3]  # strip '.py'
+#         module_path = f"{__name__}.{module_name}"
+#         module = importlib.import_module(module_path)
+#
+#         # If the module defines __all__, expose those names at utils level
+#         if hasattr(module, "__all__"):
+#             for name in module.__all__:
+#                 globals()[name] = getattr(module, name)
+#                 __all__.append(name)

geney/utils/spliceai_utils.py

@@ -1,46 +1,4 @@
-# __all__ = ['sai_predict_probs']
-#
-# #### SpliceAI Modules
-#
-# from keras.models import load_model
-# from importlib import resources
-# import numpy as np
-# import tensorflow as tf
-# import sys
-# import absl.logging
-# absl.logging.set_verbosity(absl.logging.ERROR)
-#
-#
-# # Check if GPU is available
-# # 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)
-#
-# # List the model filenames relative to the spliceai package.
-# 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]
-#
-# 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]
-
-# __all__ = ['sai_predict_probs']
+
 import os
 os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
 

{geney-1.4.4.dist-info → geney-1.4.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.4.4
+Version: 1.4.6
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.4.4.dist-info → geney-1.4.6.dist-info}/RECORD

@@ -1,5 +1,5 @@
 geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
-geney/Gene.py,sha256=G-5ROebtvbVazzPlsBJ1r2DEduCwsIA5S8_TmBuoyjw,7030
+geney/Gene.py,sha256=6x1sEZV50Il4oydegW6iHIF12EZTGexniG3YUD-3DfM,7036
 geney/Oncosplice.py,sha256=ETAvMl_Oq6mEJQHPNwdDO5csX6Ahuped_om10KifCyM,17739
 geney/SeqMats.py,sha256=9-eJnfU2w3LGc0XvVvFEO_QrBneTkC6xkZKDfTcEw5o,19282
 geney/SpliceSimulator.py,sha256=iF6feVeSnsKFmn3WV60CgWLI0_rSLgpq5fVFL1IOv_4,18491
@@ -39,13 +39,13 @@ geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUD
 geney/utils/Fasta_segment.py,sha256=weB5NJ65P0XiyAJCiCHx4T9sHC1pWLpuQeOy0B85gyg,11364
 geney/utils/SeqMats.py,sha256=vjU0lTkB0s0RoLjNXLqt0kJQDni-it09-iAOv5QAYFs,17686
 geney/utils/TranscriptLibrary.py,sha256=ma_ZVPgglxXDDneEvdqxxeqxG8eSFL-zgLUXyC6BqY8,2070
-geney/utils/__init__.py,sha256=jCoB0doidTbCFT34Yx8gQROcZOsw4LnqhgkwRgGQWt0,693
+geney/utils/__init__.py,sha256=-nJ-DMx1JzP-ZCe_QuQCeM0ZYIT_16jxoXDhUaO_4Oc,714
 geney/utils/mutation_utils.py,sha256=r-pHr56gEa5kh_DPX8MjFY3ZfYaOtyo4CUfJ5ZHlXPw,3243
 geney/utils/pangolin_utils.py,sha256=JQSPbWxdzqGFYfWQktkfLMaMSGR28eGQhNzO7MLMe5M,6162
-geney/utils/spliceai_utils.py,sha256=xju1ObxQiQ_uoca-LxS0LpeIrqPez8-r9JNnwwoxZpk,4541
+geney/utils/spliceai_utils.py,sha256=VtrIbjyQxk_3lw86eWjftRYyal9OzxArJ0GV5u_ymTg,2721
 geney/utils/splicing_utils.py,sha256=vPCGnCPR1ooEZEHR79yFHLmRQXEJHXEQjjxpBR-YWOs,20635
 geney/utils/utils.py,sha256=m51Vd0cEbrcIHo6_8BAuI9YSPcKRs22e5LfVd2Qj6Is,2181
-geney-1.4.4.dist-info/METADATA,sha256=jWA_O5yFvCaCLnzqq2hDYjpxMXGAwkA9PWhfMHaxzF0,989
-geney-1.4.4.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.4.4.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.4.4.dist-info/RECORD,,
+geney-1.4.6.dist-info/METADATA,sha256=6l8_LlR20Qo1KIhiBTve1A1kWax1IYHfYCyqv1dsMUk,989
+geney-1.4.6.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.4.6.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.4.6.dist-info/RECORD,,