geney 1.2.57__py2.py3-none-any.whl → 1.2.58__py2.py3-none-any.whl

geney/spliceai_utils.py

@@ -2,7 +2,7 @@
 #### SpliceAI Modules
 from keras.models import load_model
 from pkg_resources import resource_filename
-from spliceai.utils import one_hot_encode
+# from spliceai.utils import one_hot_encode
 import numpy as np
 import tensorflow as tf
 
@@ -12,14 +12,28 @@ if tf.config.list_physical_devices('GPU'):
 else:
     print("Running on CPU.")
 
-tf.config.threading.set_intra_op_parallelism_threads(1)
-tf.config.threading.set_inter_op_parallelism_threads(1)
+# tf.config.threading.set_intra_op_parallelism_threads(1)
+# tf.config.threading.set_inter_op_parallelism_threads(1)
 
 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]
 
 
 
+def one_hot_encode(seq):
+
+    map = np.asarray([[0, 0, 0, 0],
+                      [1, 0, 0, 0],
+                      [0, 1, 0, 0],
+                      [0, 0, 1, 0],
+                      [0, 0, 0, 1]])
+
+    seq = seq.upper().replace('A', '\x01').replace('C', '\x02')
+    seq = seq.replace('G', '\x03').replace('T', '\x04').replace('N', '\x00')
+
+    return map[np.fromstring(seq, np.int8) % 5]
+
+
 def sai_predict_probs(seq: str, models: list) -> list:
     '''
     Predicts the donor and acceptor junction probability of each

{geney-1.2.57.dist-info → geney-1.2.58.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.57
+Version: 1.2.58
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.57.dist-info → geney-1.2.58.dist-info}/RECORD

@@ -10,7 +10,7 @@ geney/oncosplice.py,sha256=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
 geney/pangolin_utils.py,sha256=HvXfdLhHWTDXNmYtc8K3p64iTvDtsBq6-Jml5tpg7JI,2930
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=2cRXT_Ox4IdzCM8x3H2HexxFZzjo5WHs0HZiUQv8fBM,18347
-geney/spliceai_utils.py,sha256=21_TaiLW3faRuPegMgsVvIf1G1a03penZSiydQ-hOTA,1869
+geney/spliceai_utils.py,sha256=WsHa0rfszTWc3Syp_an9FgJFYUvR-2vL9mZ3rVFMqb0,2275
 geney/splicing_utils.py,sha256=34xdarFpTHsHZkhi7VrHby9DaIBZ2xCLqPMrTmasEgE,16860
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
@@ -20,7 +20,7 @@ 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-1.2.57.dist-info/METADATA,sha256=UFirGNGhFN_aJnqSO8WHagJCmEfKoHdfRZojLfKymsE,948
-geney-1.2.57.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.57.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.57.dist-info/RECORD,,
+geney-1.2.58.dist-info/METADATA,sha256=2JzM2cheIg-hbdz2hy_46ltky6-VTn4qZCj0ZCNOSn0,948
+geney-1.2.58.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.58.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.58.dist-info/RECORD,,