geney 1.3.5__py2.py3-none-any.whl → 1.3.7__py2.py3-none-any.whl

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Files changed (7) hide show
  1. geney/Fasta_segment.py +1 -1
  2. geney/config_setup.py +1 -0
  3. geney/splicing_utils.py +1 -1
  4. {geney-1.3.5.dist-info → geney-1.3.7.dist-info}/METADATA +1 -1
  5. {geney-1.3.5.dist-info → geney-1.3.7.dist-info}/RECORD +7 -7
  6. {geney-1.3.5.dist-info → geney-1.3.7.dist-info}/WHEEL +0 -0
  7. {geney-1.3.5.dist-info → geney-1.3.7.dist-info}/top_level.txt +0 -0
geney/Fasta_segment.py CHANGED
@@ -104,7 +104,7 @@ class Fasta_segment():
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  indices = list(range(start_loc, end_loc + 1))
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  assert len(seq) == len(
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  indices), f'reference data not compatible; {len(seq)}, {len(indices)}, start: {start_loc}, end: {end_loc}, {file}'
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- return seq, indices
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+ return {"seq": seq, "indices": indices}
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  def __compute_file_stats(self, fp) -> tuple:
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  '''
geney/config_setup.py CHANGED
@@ -8,6 +8,7 @@ def get_config():
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  config_setup = {k: {k_in: Path(p_in) for k_in, p_in in p.items()} for k, p in json.loads(open(config_file).read()).items()}
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  config_setup['hg38']['titer_path'] = Path('/tamir2/nicolaslynn/tools/titer')
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  config_setup['hg38']['yoram_path'] = Path('/tamir2/yoramzar/Projects/Cancer_mut/Utils')
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+ config_setup['hg38']['splicing_db'] = Path('/tamir2/nicolaslynn/data/OncosplicePredictions/hg38/splicing')
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  else:
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  print("Database not set up.")
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  config_setup = {}
geney/splicing_utils.py CHANGED
@@ -495,7 +495,7 @@ import os
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  # Global connection and cursor (adjust to your architecture)
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  # Ideally, initialize this once in your application startup code.
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- DB_PATH = os.path.join(config['splicing_db'], 'mutation_data.db')
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+ DB_PATH = os.path.join(config['hg38']['splicing_db'], 'mutation_data.db')
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  conn = sqlite3.connect(DB_PATH, isolation_level=None) # autocommit mode
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  cursor = conn.cursor()
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{geney-1.3.5.dist-info → geney-1.3.7.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: 1.3.5
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+ Version: 1.3.7
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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-1.3.5.dist-info → geney-1.3.7.dist-info}/RECORD RENAMED
@@ -1,10 +1,10 @@
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- geney/Fasta_segment.py,sha256=0zCdzPUbDeM9Rz642woH5Q94pwI46O0fE3H8w0XWebc,11255
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+ geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
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  geney/Gene.py,sha256=JGWtfA6-d1W3I9YRASwaF8vaZ6CCuY0KEawQNdloIqY,6259
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  geney/SeqMats.py,sha256=jkXmXAs0OpnFeyCfiJcKKpHHSi9JpKgiOIwsu63e1CQ,18557
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  geney/Transcript.py,sha256=eRZXVVxDVBbv0l385bnAOBFRBSzBwppXcbBq8KXkwlo,14443
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  geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
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  geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
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- geney/config_setup.py,sha256=klm_k7Ca_703DpeGBcGoDqz1XwHQhNXENPKjj_xfSQw,608
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+ geney/config_setup.py,sha256=nblcGU3HIt8YjdrAoGfbEVKRxwJKv0PikJ5-7AL6axQ,723
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  geney/data_setup.py,sha256=2RHmuvcGUQbEglXQEZr0C2QPDTQYRZOEm0EcmyfQJgU,12229
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  geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
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  geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
@@ -15,7 +15,7 @@ geney/pangolin_utils.py,sha256=i5j5vEMCWOTIa1mRP2377BAhlUFZjHBzTQBips4lA_4,2934
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  geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
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  geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
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  geney/spliceai_utils.py,sha256=PFIhTK8Ihrj-cv5tgRN0UFPYEmC4uxtqXSP9bBLnZRM,3077
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- geney/splicing_utils.py,sha256=Y-yqRSlP7aRaYP9mpHLOI_1fL8nEEkRmgpfqQPslD8I,26358
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+ geney/splicing_utils.py,sha256=sDohbrEQx2cevpj6YPPPsfa-ic7R2j6RRpOlbyC5foc,26366
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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
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  geney/tis_utils.py,sha256=2makfGfVlDFVIbxzXE85AY9jmAjcNmxyIAxjvkRA5LY,7396
@@ -24,7 +24,7 @@ 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-1.3.5.dist-info/METADATA,sha256=XnLZYFIOc0OInDhB0TQOrp0rM07OatxiD8QcNNWMISg,994
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- geney-1.3.5.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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- geney-1.3.5.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.5.dist-info/RECORD,,
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+ geney-1.3.7.dist-info/METADATA,sha256=lf_Sup4GRMD5YZZUuIpO0WKbhNX5NBJ53R6AQR5AkfU,994
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+ geney-1.3.7.dist-info/WHEEL,sha256=fS9sRbCBHs7VFcwJLnLXN1MZRR0_TVTxvXKzOnaSFs8,110
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+ geney-1.3.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.7.dist-info/RECORD,,
{geney-1.3.5.dist-info → geney-1.3.7.dist-info}/WHEEL RENAMED
File without changes