geney 1.2.57__py2.py3-none-any.whl → 1.2.59__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/spliceai_utils.py +31 -6
  2. {geney-1.2.57.dist-info → geney-1.2.59.dist-info}/METADATA +1 -1
  3. {geney-1.2.57.dist-info → geney-1.2.59.dist-info}/RECORD +5 -5
  4. {geney-1.2.57.dist-info → geney-1.2.59.dist-info}/WHEEL +0 -0
  5. {geney-1.2.57.dist-info → geney-1.2.59.dist-info}/top_level.txt +0 -0
geney/spliceai_utils.py CHANGED
@@ -1,10 +1,12 @@
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  #### SpliceAI Modules
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  from keras.models import load_model
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- from pkg_resources import resource_filename
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- from spliceai.utils import one_hot_encode
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+ # from pkg_resources import resource_filename
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+ from importlib import resources
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+ # from spliceai.utils import one_hot_encode
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  import numpy as np
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  import tensorflow as tf
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+ import sys
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  # Check if GPU is available
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  if tf.config.list_physical_devices('GPU'):
@@ -12,12 +14,35 @@ if tf.config.list_physical_devices('GPU'):
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  else:
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  print("Running on CPU.")
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- tf.config.threading.set_intra_op_parallelism_threads(1)
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- tf.config.threading.set_inter_op_parallelism_threads(1)
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+ # tf.config.threading.set_intra_op_parallelism_threads(1)
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+ # tf.config.threading.set_inter_op_parallelism_threads(1)
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- sai_paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))
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- sai_models = [load_model(resource_filename('spliceai', x)) for x in sai_paths]
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+ if sys.platform == 'darwin':
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+ sai_paths = ('models/spliceai{}.h5'.format(x) for x in range(1, 6))
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+ # sai_models = [load_model(resource_filename('spliceai', x)) for x in sai_paths]
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+ sai_models = [load_model(resources.files('spliceai').joinpath(f)) for f in sai_paths]
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+ else:
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+ sai_paths = ['/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai1.h5',
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+ '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai2.h5',
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+ '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai3.h5',
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+ '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai4.h5',
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+ '/tamir2/nicolaslynn/home/miniconda3/lib/python3.10/site-packages/spliceai/models/spliceai5.h5']
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+
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+ sai_models = [load_model(f) for f in sai_paths]
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+
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+
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+ def one_hot_encode(seq):
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+
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+ map = np.asarray([[0, 0, 0, 0],
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+ [1, 0, 0, 0],
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+ [0, 1, 0, 0],
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+ [0, 0, 1, 0],
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+ [0, 0, 0, 1]])
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+
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+ seq = seq.upper().replace('A', '\x01').replace('C', '\x02')
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+ seq = seq.replace('G', '\x03').replace('T', '\x04').replace('N', '\x00')
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+ return map[np.fromstring(seq, np.int8) % 5]
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  def sai_predict_probs(seq: str, models: list) -> list:
{geney-1.2.57.dist-info → geney-1.2.59.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: geney
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- Version: 1.2.57
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+ Version: 1.2.59
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  Summary: A Python package for gene expression modeling.
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  Home-page: https://github.com/nicolaslynn/geney
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  Author: Nicolas Lynn
{geney-1.2.57.dist-info → geney-1.2.59.dist-info}/RECORD RENAMED
@@ -10,7 +10,7 @@ geney/oncosplice.py,sha256=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
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  geney/pangolin_utils.py,sha256=HvXfdLhHWTDXNmYtc8K3p64iTvDtsBq6-Jml5tpg7JI,2930
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  geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
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  geney/seqmat_utils.py,sha256=2cRXT_Ox4IdzCM8x3H2HexxFZzjo5WHs0HZiUQv8fBM,18347
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- geney/spliceai_utils.py,sha256=21_TaiLW3faRuPegMgsVvIf1G1a03penZSiydQ-hOTA,1869
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+ geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
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  geney/splicing_utils.py,sha256=34xdarFpTHsHZkhi7VrHby9DaIBZ2xCLqPMrTmasEgE,16860
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  geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
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  geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
@@ -20,7 +20,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
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  geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
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  geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
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  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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- geney-1.2.57.dist-info/METADATA,sha256=UFirGNGhFN_aJnqSO8WHagJCmEfKoHdfRZojLfKymsE,948
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- geney-1.2.57.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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- geney-1.2.57.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.2.57.dist-info/RECORD,,
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+ geney-1.2.59.dist-info/METADATA,sha256=fiwDiB2jrpokLcoAhC6YQ2OQyY6RBdJSjhQx_T99lXo,948
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+ geney-1.2.59.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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+ geney-1.2.59.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.2.59.dist-info/RECORD,,
{geney-1.2.57.dist-info → geney-1.2.59.dist-info}/WHEEL RENAMED
File without changes