pytransdecoder 0.2.1__py3-none-any.whl

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Files changed (63) hide show
  1. pytransdecoder/__init__.py +7 -0
  2. pytransdecoder/__main__.py +6 -0
  3. pytransdecoder/cli.py +781 -0
  4. pytransdecoder/core/__init__.py +1 -0
  5. pytransdecoder/core/base_freqs.py +71 -0
  6. pytransdecoder/core/decoys.py +113 -0
  7. pytransdecoder/core/fasta.py +55 -0
  8. pytransdecoder/core/gene_model.py +143 -0
  9. pytransdecoder/core/gff3_parser.py +58 -0
  10. pytransdecoder/core/homology_starts.py +54 -0
  11. pytransdecoder/core/kozak.py +180 -0
  12. pytransdecoder/core/models.py +123 -0
  13. pytransdecoder/core/orf_finder.py +317 -0
  14. pytransdecoder/core/presets.py +152 -0
  15. pytransdecoder/core/prng.py +54 -0
  16. pytransdecoder/core/pwm.py +174 -0
  17. pytransdecoder/core/sequence.py +19 -0
  18. pytransdecoder/core/translator.py +143 -0
  19. pytransdecoder/core/writers.py +69 -0
  20. pytransdecoder/genome.py +338 -0
  21. pytransdecoder/longorfs.py +180 -0
  22. pytransdecoder/predict.py +1621 -0
  23. pytransdecoder/presets/apicomplexan/hexamer.scores.gz +0 -0
  24. pytransdecoder/presets/apicomplexan/kozak.tsv +9 -0
  25. pytransdecoder/presets/apicomplexan/preset.json +20 -0
  26. pytransdecoder/presets/apicomplexan/thresholds.tsv.gz +0 -0
  27. pytransdecoder/presets/apicomplexan/training_orfs.cds.gz +0 -0
  28. pytransdecoder/presets/ciliate/hexamer.scores.gz +0 -0
  29. pytransdecoder/presets/ciliate/kozak.tsv +9 -0
  30. pytransdecoder/presets/ciliate/preset.json +20 -0
  31. pytransdecoder/presets/ciliate/thresholds.tsv.gz +0 -0
  32. pytransdecoder/presets/ciliate/training_orfs.cds.gz +0 -0
  33. pytransdecoder/presets/fungus/hexamer.scores.gz +0 -0
  34. pytransdecoder/presets/fungus/kozak.tsv +9 -0
  35. pytransdecoder/presets/fungus/preset.json +20 -0
  36. pytransdecoder/presets/fungus/thresholds.tsv.gz +0 -0
  37. pytransdecoder/presets/fungus/training_orfs.cds.gz +0 -0
  38. pytransdecoder/presets/green_alga/hexamer.scores.gz +0 -0
  39. pytransdecoder/presets/green_alga/kozak.tsv +9 -0
  40. pytransdecoder/presets/green_alga/preset.json +20 -0
  41. pytransdecoder/presets/green_alga/thresholds.tsv.gz +0 -0
  42. pytransdecoder/presets/green_alga/training_orfs.cds.gz +0 -0
  43. pytransdecoder/presets/insect/hexamer.scores.gz +0 -0
  44. pytransdecoder/presets/insect/kozak.tsv +9 -0
  45. pytransdecoder/presets/insect/preset.json +20 -0
  46. pytransdecoder/presets/insect/thresholds.tsv.gz +0 -0
  47. pytransdecoder/presets/insect/training_orfs.cds.gz +0 -0
  48. pytransdecoder/presets/mammal/hexamer.scores.gz +0 -0
  49. pytransdecoder/presets/mammal/kozak.tsv +9 -0
  50. pytransdecoder/presets/mammal/preset.json +20 -0
  51. pytransdecoder/presets/mammal/thresholds.tsv.gz +0 -0
  52. pytransdecoder/presets/mammal/training_orfs.cds.gz +0 -0
  53. pytransdecoder/presets/plant/hexamer.scores.gz +0 -0
  54. pytransdecoder/presets/plant/kozak.tsv +9 -0
  55. pytransdecoder/presets/plant/preset.json +20 -0
  56. pytransdecoder/presets/plant/thresholds.tsv.gz +0 -0
  57. pytransdecoder/presets/plant/training_orfs.cds.gz +0 -0
  58. pytransdecoder-0.2.1.dist-info/METADATA +307 -0
  59. pytransdecoder-0.2.1.dist-info/RECORD +63 -0
  60. pytransdecoder-0.2.1.dist-info/WHEEL +5 -0
  61. pytransdecoder-0.2.1.dist-info/entry_points.txt +3 -0
  62. pytransdecoder-0.2.1.dist-info/licenses/LICENSE +28 -0
  63. pytransdecoder-0.2.1.dist-info/top_level.txt +1 -0
pytransdecoder/__init__.py ADDED
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+ """
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+ PyTransDecoder - Python port of TransDecoder
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+
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+ Identifies candidate protein-coding regions within transcript sequences.
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+ """
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+
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+ __version__ = "0.2.1"
pytransdecoder/__main__.py ADDED
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+ """Entry point for python -m pytransdecoder"""
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+
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+ from .cli import cli
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+
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+ if __name__ == '__main__':
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+ cli()