geney 1.2.58__py2.py3-none-any.whl → 1.2.60__py2.py3-none-any.whl

geney/pangolin_utils.py

@@ -52,6 +52,7 @@ def pangolin_predict_probs(true_seq, models, just_ss=False):
         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/seqmat_utils.py

@@ -3,7 +3,7 @@ import numpy as np
 import copy
 from Bio.Seq import Seq
 
-NT_ALPHABET = ['A', 'T', 'G', 'C']
+NT_ALPHABET = ['A', 'T', 'G', 'C', 'N']
 
 
 '''
@@ -119,7 +119,6 @@ class SeqMat:
 
     @property
     def seq(self):
-
         return ''.join(self.vectorized_map_v2c(self.seqmat[self.ROW_SEQ, :])).replace('-', '')
 
     @property

geney/spliceai_utils.py

@@ -1,10 +1,12 @@
 
 #### SpliceAI Modules
 from keras.models import load_model
-from pkg_resources import resource_filename
+# from pkg_resources import resource_filename
+from importlib import resources
 # from spliceai.utils import one_hot_encode
 import numpy as np
 import tensorflow as tf
+import sys
 
 # Check if GPU is available
 if tf.config.list_physical_devices('GPU'):
@@ -15,9 +17,18 @@ else:
 # 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]
+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]
 
 
 def one_hot_encode(seq):

geney/splicing_utils.py

@@ -358,3 +358,40 @@ def missplicing(mut_id, splicing_threshold=0.5, primary_transcript=True, organis
 
     return results
 
+
+import sqlite3
+import json
+
+def get_or_compute_splicing(tool, gene, mutation_id, transcript_id, force_recompute=False):
+    conn = sqlite3.connect(os.path.join(tool_parameters['splicing_db'], 'mutation_data.db'))
+    cursor = conn.cursor()
+    # Create table if it doesn't exist
+    cursor.execute('''CREATE TABLE IF NOT EXISTS mutations (
+                         tool TEXT,
+                         gene TEXT,
+                         mutation_id TEXT, 
+                         transcript_id TEXT, 
+                         data TEXT,
+                         PRIMARY KEY (tool, gene, mutation_id, transcript_id)
+                      )''')
+
+    # Look up entry
+    cursor.execute('SELECT data FROM mutations WHERE tool=? AND gene=? AND mutation_id=? AND transcript_id=?',
+                   (tool, gene, mutation_id, transcript_id))
+    row = cursor.fetchone()
+
+    # If entry is found and force_recompute is False, return data
+    if row and not force_recompute:
+        return json.loads(row[0])
+
+    # Otherwise, compute the dictionary
+    computed_data = find_transcript_missplicing(tool, mutation_id, transcript_id)  # Replace with actual function
+
+    # Store in the database
+    data_json = json.dumps(computed_data)
+    cursor.execute('REPLACE INTO mutations (tool, mutation_id, transcript_id, data) VALUES (?, ?, ?, ?)',
+                   (tool, mutation_id, transcript_id, data_json))
+    conn.commit()
+    conn.close()
+
+    return computed_data

{geney-1.2.58.dist-info → geney-1.2.60.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.2.58
+Version: 1.2.60
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.2.58.dist-info → geney-1.2.60.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=HvXfdLhHWTDXNmYtc8K3p64iTvDtsBq6-Jml5tpg7JI,2930
+geney/pangolin_utils.py,sha256=Hsq9Y_GLFHGqEDn25_VdD7YKUYxpjMlynj0z-B_LezE,2931
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
-geney/seqmat_utils.py,sha256=2cRXT_Ox4IdzCM8x3H2HexxFZzjo5WHs0HZiUQv8fBM,18347
-geney/spliceai_utils.py,sha256=WsHa0rfszTWc3Syp_an9FgJFYUvR-2vL9mZ3rVFMqb0,2275
-geney/splicing_utils.py,sha256=34xdarFpTHsHZkhi7VrHby9DaIBZ2xCLqPMrTmasEgE,16860
+geney/seqmat_utils.py,sha256=hIikPuybVdZ3ZU9WlaTs6ON7U0AVQv5Kya4CXhKIt-s,18351
+geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
+geney/splicing_utils.py,sha256=I_YKc5O0djYY5VgDqBb0JFYogPEUyH6n9B_IngAw33Y,18321
 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-1.2.58.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,,
+geney-1.2.60.dist-info/METADATA,sha256=hot8OpcKUrw3KWJcUS8NtgHvggVmM9CSNteWAinAVls,948
+geney-1.2.60.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
+geney-1.2.60.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.2.60.dist-info/RECORD,,