geney 1.2.6__py2.py3-none-any.whl → 1.2.7__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/oncosplice.py +6 -2
  2. {geney-1.2.6.dist-info → geney-1.2.7.dist-info}/METADATA +1 -1
  3. {geney-1.2.6.dist-info → geney-1.2.7.dist-info}/RECORD +5 -5
  4. {geney-1.2.6.dist-info → geney-1.2.7.dist-info}/WHEEL +0 -0
  5. {geney-1.2.6.dist-info → geney-1.2.7.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -1013,7 +1013,7 @@ def find_transcript_missplicing(mutations, ref_transcript, var_transcript, conte
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  class PredictSpliceAI:
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  def __init__(self, mutation, gene_data,
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- threshold=0.5, force=False, save_results=False, sai_mrg_context=5000, min_coverage=2500):
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+ threshold=0.5, force=False, save_results=False, sai_mrg_context=5000, min_coverage=2500, engine='spliceai'):
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  self.modification = mutation
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  self.threshold = threshold
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  self.transcript_id = gene_data.transcript_id
@@ -1031,7 +1031,11 @@ class PredictSpliceAI:
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  # self.save_sai_predictions()
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  #
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  # elif isinstance(gene_data, Transcript):
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- self.missplicing = run_spliceai_transcript(self.modification, transcript_data=gene_data, sai_mrg_context=sai_mrg_context, min_coverage=min_coverage, sai_threshold=0.1)
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+
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+ # self.missplicing = run_spliceai_transcript(self.modification, transcript_data=gene_data, sai_mrg_context=sai_mrg_context, min_coverage=min_coverage, sai_threshold=0.1)
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+ ref_transcript, var_transcript = Gene(gene_data.gene, organism='mm39'), Gene(gene_data.gene, variation=mutation, organism='mm39')
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+ self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
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+ engine=engine)
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  if save_results:
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  self.save_sai_predictions()
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{geney-1.2.6.dist-info → geney-1.2.7.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: 1.2.6
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+ Version: 1.2.7
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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-1.2.6.dist-info → geney-1.2.7.dist-info}/RECORD RENAMED
@@ -9,7 +9,7 @@ geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
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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/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
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- geney/oncosplice.py,sha256=aaOxri0bXLPfB3Mu8tkzk4KEVlzzocImzj3MI-0uU_0,76949
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+ geney/oncosplice.py,sha256=8tV8Wzz_I3CNGgeNNqhJvDOb1A3slzsyk9mnRQXuC-c,77329
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  geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
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  geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
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  geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -45,7 +45,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
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  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
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  geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- geney-1.2.6.dist-info/METADATA,sha256=hcHNz2oNxRLzNpimwrHeM2yKSnd1z5KHJ_Rl86LD3QE,1198
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- geney-1.2.6.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
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- geney-1.2.6.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.2.6.dist-info/RECORD,,
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+ geney-1.2.7.dist-info/METADATA,sha256=cCD7LSrUBVp3Hr7HtUFTEFuKFAeD1Yq3Zoyh31CZTfk,1198
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+ geney-1.2.7.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
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+ geney-1.2.7.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.2.7.dist-info/RECORD,,
{geney-1.2.6.dist-info → geney-1.2.7.dist-info}/WHEEL RENAMED
File without changes