geney 1.3.78__py2.py3-none-any.whl → 1.4.0__py2.py3-none-any.whl

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Files changed (32) hide show
  1. geney/Gene.py +9 -10
  2. geney/Oncosplice.py +400 -0
  3. geney/SpliceSimulator.py +407 -0
  4. geney/Transcript.py +55 -57
  5. geney/__init__.py +47 -19
  6. geney/_config_setup.py +16 -0
  7. geney/_graphic_utils.py +269 -0
  8. geney/_gtex_utils.py +68 -0
  9. geney/_immune_utils.py +125 -0
  10. geney/{oncosplice.py → _oncosplice.py} +199 -156
  11. geney/_splicing_utils.py +693 -0
  12. geney/_survival_utils.py +143 -0
  13. geney/_tcga_utils.py +405 -0
  14. geney/_tis_utils.py +172 -0
  15. geney/immune_utils.py +1 -1
  16. geney/pipelines.py +66 -0
  17. geney/power_utils.py +1 -1
  18. geney/spliceai_utils.py +17 -17
  19. geney/utils/Fasta_segment.py +260 -0
  20. geney/utils/SeqMats.py +423 -0
  21. geney/utils/TranscriptLibrary.py +55 -0
  22. geney/utils/__init__.py +20 -0
  23. geney/utils/mutation_utils.py +104 -0
  24. geney/utils/pangolin_utils.py +173 -0
  25. geney/utils/spliceai_utils.py +123 -0
  26. geney/utils/splicing_utils.py +525 -0
  27. geney/utils/utils.py +89 -0
  28. {geney-1.3.78.dist-info → geney-1.4.0.dist-info}/METADATA +1 -1
  29. geney-1.4.0.dist-info/RECORD +51 -0
  30. {geney-1.3.78.dist-info → geney-1.4.0.dist-info}/WHEEL +1 -1
  31. geney-1.3.78.dist-info/RECORD +0 -31
  32. {geney-1.3.78.dist-info → geney-1.4.0.dist-info}/top_level.txt +0 -0
geney-1.3.78.dist-info/RECORD DELETED
@@ -1,31 +0,0 @@
1
- geney/Fasta_segment.py,sha256=99HxNGNh_MfdVW6hhtlb1vOn7eSmT7oFoEfHDFMxG8w,11275
2
- geney/Gene.py,sha256=2eznhavDoO4rktisy3U0uz480OsktppEwH5pxC2qoog,7083
3
- geney/SeqMats.py,sha256=9-eJnfU2w3LGc0XvVvFEO_QrBneTkC6xkZKDfTcEw5o,19282
4
- geney/Transcript.py,sha256=CpfxYkuCwFILozrtLuiWnlr1mRnMKn4o84HVJislgYs,14499
5
- geney/__init__.py,sha256=eBdDl42N6UhcYeZDjOnv199Z88fI5_8Y6xW8447OKXM,755
6
- geney/_mutation_utils.py,sha256=dHssUsnii_mf-wuRoMmF13UlD7k3ml_VwQMItTYnXpU,1132
7
- geney/allele_linkage.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
8
- geney/config_setup.py,sha256=nblcGU3HIt8YjdrAoGfbEVKRxwJKv0PikJ5-7AL6axQ,723
9
- geney/data_setup.py,sha256=2RHmuvcGUQbEglXQEZr0C2QPDTQYRZOEm0EcmyfQJgU,12229
10
- geney/graphic_utils.py,sha256=oMsBpB9YeEn96gGpKh4MmtagJffWZbk-xPrIwHvkFhA,11016
11
- geney/gtex_utils.py,sha256=asL2lHyU5KsbWpV096vkf1Ka7hSo_RRfZqw7p5nERmE,1919
12
- geney/immune_utils.py,sha256=ZRni5ttrhpYBnmNr0d0ZatIbNPYs4nmQuoUO00SpsS4,5271
13
- geney/mutation_utils.py,sha256=C_kv2MB_L8LlhX3W2ooXjJ3uDoJ8zX1WeDtZKoBZJkI,1547
14
- geney/oncosplice.py,sha256=7KpuvIMLEZ4VGPIOw-UUwiPGfQgeFVrapqNt6jLreRA,32308
15
- geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
16
- geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
17
- geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
18
- geney/spliceai_utils.py,sha256=V5DccGjm2GZQINSVxJYPoN8iYQzU4gE9tINy6gmHjOM,3304
19
- geney/splicing_utils.py,sha256=UkG2YphjLNUYsv3o3RGUTW1ScHbEMOLL2M_7WbgDVME,47466
20
- geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
21
- geney/tcga_utils.py,sha256=uJhVnTbTysj0XrEw_YeDKRSLexsqgBLYQdhl7_hnr64,17611
22
- geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
23
- geney/utils.py,sha256=KBdwNIywo7INVEQEsuIXauEJobvReE9TXAi5qqXanSI,2775
24
- geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
25
- geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
26
- geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
27
- geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
28
- geney-1.3.78.dist-info/METADATA,sha256=0OGHLbmr98kR8Q8FNmmnbjVBIv9a-TObHTMUDnG_2EM,990
29
- geney-1.3.78.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
30
- geney-1.3.78.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
31
- geney-1.3.78.dist-info/RECORD,,