geney 1.3.35__py2.py3-none-any.whl → 1.3.37__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/oncosplice.py +2 -2
  2. {geney-1.3.35.dist-info → geney-1.3.37.dist-info}/METADATA +1 -1
  3. {geney-1.3.35.dist-info → geney-1.3.37.dist-info}/RECORD +5 -5
  4. {geney-1.3.35.dist-info → geney-1.3.37.dist-info}/WHEEL +0 -0
  5. {geney-1.3.35.dist-info → geney-1.3.37.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -340,7 +340,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
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  else:
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  missplicing, no_splicing_record = None, True
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  if splicing_db is not None:
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- missplicing = splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene, transcript_id=reference_transcript.transcript_id)
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+ missplicing = splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene.gene_name, transcript_id=reference_transcript.transcript_id)
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  no_splicing_record = missplicing is None
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  if missplicing is None:
@@ -349,7 +349,7 @@ def oncosplice(mut_id, splicing_threshold=0.5, protein_coding=True, cons_require
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  mutated_transcript.pre_mrna.get_context(center, context=7500, padding='N'), reference_transcript.donors,
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  reference_transcript.acceptors, threshold=splicing_threshold, engine=splicing_engine)
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  if no_splicing_record and splicing_db is not None:
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- splicing_db.get_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene, transcript_id=reference_transcript.transcript_id, data=missplicing.missplicing)
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+ splicing_db.store_mutation_data(engine=splicing_engine, mut_id=mut_id, gene=gene.gene_name, transcript_id=reference_transcript.transcript_id, data=missplicing.missplicing)
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  alternative_splicing_paths = develop_aberrant_splicing(reference_transcript, missplicing.aberrant_splicing)
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  for i, new_boundaries in enumerate(alternative_splicing_paths):
{geney-1.3.35.dist-info → geney-1.3.37.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: 1.3.35
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+ Version: 1.3.37
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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-1.3.35.dist-info → geney-1.3.37.dist-info}/RECORD RENAMED
@@ -11,7 +11,7 @@ geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
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  geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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  geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
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  geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
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- geney/oncosplice.py,sha256=3_XAUbzpCTYBI9W1uag75ed93lsNw8UuvnM6LjwTXZY,23221
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+ geney/oncosplice.py,sha256=GNxbofZ84aEU9MxmV223S2AzT4ZxFe3azumX0sKImYs,23243
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  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
@@ -25,7 +25,7 @@ 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-1.3.35.dist-info/METADATA,sha256=yhGQQBVx7g7hjOBXPgMZMb5-R9gfnnpjFVNWnRJuPwQ,990
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- geney-1.3.35.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.3.35.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.35.dist-info/RECORD,,
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+ geney-1.3.37.dist-info/METADATA,sha256=s_ozaSGvJtbWOKfF7vTyJSa0UjUm_ssmf5YOdGQQ_Yw,990
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+ geney-1.3.37.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.3.37.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.37.dist-info/RECORD,,
{geney-1.3.35.dist-info → geney-1.3.37.dist-info}/WHEEL RENAMED
File without changes