geney 1.2.56__py2.py3-none-any.whl → 1.2.58__py2.py3-none-any.whl

geney/pangolin_utils.py

@@ -46,10 +46,12 @@ def pang_one_hot_encode(seq):
 
 
 
-def pangolin_predict_probs(true_seq, models):
+def pangolin_predict_probs(true_seq, models, just_ss=False):
     # print(f"Running pangolin on: {true_seq}")
-    model_nums = [0, 2, 4, 6]
-    model_nums = [0, 1, 2, 3, 4, 5, 6]
+    if just_ss:
+        model_nums = [0, 2, 4, 6]
+    else:
+        model_nums = [0, 1, 2, 3, 4, 5, 6, 7]
     INDEX_MAP = {0: 1, 1: 2, 2: 4, 3: 5, 4: 7, 5: 8, 6: 10, 7: 11}
 
     seq = true_seq

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/splicing_utils.py

@@ -145,7 +145,7 @@ def find_ss_changes(ref_dct, mut_dct, known_splice_sites, threshold=0.5):
     return discovered_pos, deleted_pos
 
 
-def find_transcript_missplicing(transcript, mutations, context=5000, window=2500, threshold=0.5, engine='spliceai'):
+def find_transcript_missplicing(transcript, mutations, context=5000, window=2500, threshold=0.5, engine='spliceai', just_ss=False):
     from functools import reduce
     ref = transcript.pre_mrna
     var = reduce(lambda acc, mutation: acc + mutation, mutations, ref)
@@ -182,8 +182,8 @@ def find_transcript_missplicing(transcript, mutations, context=5000, window=2500
 
     elif engine == 'pangolin':
         from .pangolin_utils import pangolin_predict_probs, pang_models
-        ref_seq_donor_probs, ref_seq_acceptor_probs = pangolin_predict_probs(ref_seq, models=pang_models)
-        mut_seq_donor_probs, mut_seq_acceptor_probs = pangolin_predict_probs(var_seq, models=pang_models)
+        ref_seq_donor_probs, ref_seq_acceptor_probs = pangolin_predict_probs(ref_seq, models=pang_models, just_ss=just_ss)
+        mut_seq_donor_probs, mut_seq_acceptor_probs = pangolin_predict_probs(var_seq, models=pang_models, just_ss=just_ss)
 
     else:
         raise ValueError(f"{engine} not implemented")

{geney-1.2.56.dist-info → geney-1.2.58.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.56
+Version: 1.2.58
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.56.dist-info → geney-1.2.58.dist-info}/RECORD

@@ -7,11 +7,11 @@ 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=eWgY2Lcj894UBFnIVhbxiVz5oqASHg-Ot1wFbjlJbI8,21857
-geney/pangolin_utils.py,sha256=NJEdY43L_2lielY1hZOjlak0baHqXTa1ITrvx8Tkg5o,2878
+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/splicing_utils.py,sha256=t0vE5KTAdYOYJLa9wjaSJ1jqiHhsDxZs64OxrgR-Sqc,16811
+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
 geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -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-1.2.56.dist-info/METADATA,sha256=tHCFJyD9OKjk7GnQToKesLQZyzy0dtO9oBsr0Bjz6rI,948
-geney-1.2.56.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
-geney-1.2.56.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.2.56.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,,