geney 1.3.77__py2.py3-none-any.whl → 1.3.78__py2.py3-none-any.whl

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Files changed (5) hide show
  1. geney/oncosplice.py +2 -3
  2. {geney-1.3.77.dist-info → geney-1.3.78.dist-info}/METADATA +1 -1
  3. {geney-1.3.77.dist-info → geney-1.3.78.dist-info}/RECORD +5 -5
  4. {geney-1.3.77.dist-info → geney-1.3.78.dist-info}/WHEEL +0 -0
  5. {geney-1.3.77.dist-info → geney-1.3.78.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -286,7 +286,7 @@ def summarize_missplicing_event(pes, pir, es, ne, ir):
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  def missense_effect(r, v):
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  nt_changes, aa_changes = '', ''
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  if len(r.protein) != len(v.protein) or len(r.orf) != len(v.orf):
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- return '', '', -1
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+ return '', ''
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  if r.protein != v.protein:
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  for i, (x, y) in enumerate(zip(r.protein, v.protein)):
@@ -318,10 +318,9 @@ def OncospliceAnnotator(reference_transcript, variant_transcript, mut, ref_attri
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  report['affected_intron'] = affected_intron
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  report['mutation_distance_from_5'] = distance_from_5
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  report['mutation_distance_from_3'] = distance_from_3
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- aa_c, c_c, pos = missense_effect(reference_transcript, variant_transcript)
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+ aa_c, c_c = missense_effect(reference_transcript, variant_transcript)
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  report['missense_effect'] = aa_c
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  report['codon_change'] = c_c
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- report['missense_position'] = pos
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  return report
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{geney-1.3.77.dist-info → geney-1.3.78.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: 1.3.77
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+ Version: 1.3.78
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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-1.3.77.dist-info → geney-1.3.78.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=hADoNLoIt_f6O2lnFL0YpIOam3mOBy0BLJUNzV4npoc,32355
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+ geney/oncosplice.py,sha256=7KpuvIMLEZ4VGPIOw-UUwiPGfQgeFVrapqNt6jLreRA,32308
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  geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
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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-1.3.77.dist-info/METADATA,sha256=7eMKlyiIIgYM794hncNt_lj1fyK6KzWc5zbTb8O4bw0,990
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- geney-1.3.77.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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- geney-1.3.77.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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- geney-1.3.77.dist-info/RECORD,,
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+ geney-1.3.78.dist-info/METADATA,sha256=0OGHLbmr98kR8Q8FNmmnbjVBIv9a-TObHTMUDnG_2EM,990
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+ geney-1.3.78.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
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+ geney-1.3.78.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
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+ geney-1.3.78.dist-info/RECORD,,
{geney-1.3.77.dist-info → geney-1.3.78.dist-info}/WHEEL RENAMED
File without changes