geney 1.2.8__py2.py3-none-any.whl → 1.2.10__py2.py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of geney might be problematic. Click here for more details.

Files changed (5) hide show
  1. geney/oncosplice.py +2 -1
  2. {geney-1.2.8.dist-info → geney-1.2.10.dist-info}/METADATA +1 -1
  3. {geney-1.2.8.dist-info → geney-1.2.10.dist-info}/RECORD +5 -5
  4. {geney-1.2.8.dist-info → geney-1.2.10.dist-info}/WHEEL +0 -0
  5. {geney-1.2.8.dist-info → geney-1.2.10.dist-info}/top_level.txt +0 -0
geney/oncosplice.py CHANGED
@@ -519,6 +519,7 @@ class Transcript:
519
519
  seq, indices = self.pull_pre_mrna_pos()
520
520
  if self.variations:
521
521
  for mutation in self.variations.variants:
522
+ print(f"Implementing {mutation}")
522
523
  seq, indices = generate_mut_variant(seq, indices, mut=mutation)
523
524
  return seq, indices
524
525
 
@@ -1033,7 +1034,7 @@ class PredictSpliceAI:
1033
1034
  # elif isinstance(gene_data, Transcript):
1034
1035
 
1035
1036
  # 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)
1036
- ref_transcript, var_transcript = Gene(mutation.split(':')[0], organism='mm39'), Gene(mutation.split(':')[0], variation=mutation, organism='mm39')
1037
+ ref_transcript, var_transcript = Gene(mutation.mut_id.split(':')[0], organism='mm39').transcript(gene_data.transcript_id), Gene(mutation.mut_id.split(':')[0], variation=mutation, organism='mm39').transcript(gene_data.transcript_id)
1037
1038
  self.missplicing = find_transcript_missplicing(self.modification, ref_transcript, var_transcript, context=sai_mrg_context+min_coverage, threshold=threshold,
1038
1039
  engine=engine)
1039
1040
  if save_results:
{geney-1.2.8.dist-info → geney-1.2.10.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: geney
3
- Version: 1.2.8
3
+ Version: 1.2.10
4
4
  Summary: A Python package for gene expression modeling.
5
5
  Home-page: https://github.com/nicolaslynn/geney
6
6
  Author: Nicolas Lynn
{geney-1.2.8.dist-info → geney-1.2.10.dist-info}/RECORD RENAMED
@@ -9,7 +9,7 @@ geney/gtex.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
9
9
  geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
10
10
  geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
11
11
  geney/netchop.py,sha256=AMiy9YsdTmX4B3k3Y5Yh7EmoGAojM1O3AzhPKOiB--g,3050
12
- geney/oncosplice.py,sha256=NhC164g0hzuV-hxMwlVtpXFxp067Mq_fnQUhn6vKK5A,77379
12
+ geney/oncosplice.py,sha256=2m1S53RjKU9cyvEMZL98ikz9Ot05DqWe4gdensy3UAY,77515
13
13
  geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
14
14
  geney/oncosplice_pipeline.py,sha256=hpGqFHOdn8i8tvvs1-t3-G9Ko18zInwoDXBJbbrfbC4,68036
15
15
  geney/performance_utils.py,sha256=FQt7rA4r-Wuq3kceCxsSuMfj3wU1tMG8QnbL59aBohs,4700
@@ -45,7 +45,7 @@ geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFW
45
45
  geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
46
46
  geney/translation_termination/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
47
47
  geney/translation_termination/tts_utils.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
48
- geney-1.2.8.dist-info/METADATA,sha256=2Eu8FxQqLudUMoNG0rt-l2OwT8cikYNb1S407dsYG7E,1198
49
- geney-1.2.8.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
50
- geney-1.2.8.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
51
- geney-1.2.8.dist-info/RECORD,,
48
+ geney-1.2.10.dist-info/METADATA,sha256=XGHIYg4PCphwI7GbxOnHCQ7iZuUopL_3PenIkoz-HfM,1199
49
+ geney-1.2.10.dist-info/WHEEL,sha256=iYlv5fX357PQyRT2o6tw1bN-YcKFFHKqB_LwHO5wP-g,110
50
+ geney-1.2.10.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
51
+ geney-1.2.10.dist-info/RECORD,,
{geney-1.2.8.dist-info → geney-1.2.10.dist-info}/WHEEL RENAMED
File without changes