risearch 3.0.0a4__tar.gz

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.
Files changed (86) hide show
  1. risearch-3.0.0a4/CITATION.cff +35 -0
  2. risearch-3.0.0a4/Cargo.lock +2128 -0
  3. risearch-3.0.0a4/Cargo.toml +112 -0
  4. risearch-3.0.0a4/LICENSE +72 -0
  5. risearch-3.0.0a4/PKG-INFO +112 -0
  6. risearch-3.0.0a4/README.md +152 -0
  7. risearch-3.0.0a4/benches/dp.rs +302 -0
  8. risearch-3.0.0a4/benches/format.rs +79 -0
  9. risearch-3.0.0a4/benches/search.rs +240 -0
  10. risearch-3.0.0a4/benches/seed.rs +238 -0
  11. risearch-3.0.0a4/bindings/python/Cargo.toml +31 -0
  12. risearch-3.0.0a4/bindings/python/README.md +79 -0
  13. risearch-3.0.0a4/bindings/python/src/arrow.rs +117 -0
  14. risearch-3.0.0a4/bindings/python/src/error.rs +50 -0
  15. risearch-3.0.0a4/bindings/python/src/lib.rs +353 -0
  16. risearch-3.0.0a4/build.rs +5 -0
  17. risearch-3.0.0a4/pyproject.toml +82 -0
  18. risearch-3.0.0a4/risearch/__init__.py +10 -0
  19. risearch-3.0.0a4/risearch/_api.py +182 -0
  20. risearch-3.0.0a4/risearch/py.typed +0 -0
  21. risearch-3.0.0a4/src/adapter/gotoh.rs +253 -0
  22. risearch-3.0.0a4/src/adapter/mod.rs +1 -0
  23. risearch-3.0.0a4/src/alignment.rs +220 -0
  24. risearch-3.0.0a4/src/cli/app.rs +122 -0
  25. risearch-3.0.0a4/src/cli/args/extend.rs +28 -0
  26. risearch-3.0.0a4/src/cli/args/filter.rs +39 -0
  27. risearch-3.0.0a4/src/cli/args/input.rs +57 -0
  28. risearch-3.0.0a4/src/cli/args/mod.rs +16 -0
  29. risearch-3.0.0a4/src/cli/args/output.rs +262 -0
  30. risearch-3.0.0a4/src/cli/args/score.rs +114 -0
  31. risearch-3.0.0a4/src/cli/args/search.rs +47 -0
  32. risearch-3.0.0a4/src/cli/args/seed.rs +506 -0
  33. risearch-3.0.0a4/src/cli/mod.rs +76 -0
  34. risearch-3.0.0a4/src/config/mod.rs +431 -0
  35. risearch-3.0.0a4/src/config/spec_tests.rs +274 -0
  36. risearch-3.0.0a4/src/dp/core.rs +105 -0
  37. risearch-3.0.0a4/src/dp/gotoh.rs +296 -0
  38. risearch-3.0.0a4/src/dp/init.rs +260 -0
  39. risearch-3.0.0a4/src/dp/mod.rs +204 -0
  40. risearch-3.0.0a4/src/dp/reference_tests.rs +516 -0
  41. risearch-3.0.0a4/src/dp/scoring.rs +61 -0
  42. risearch-3.0.0a4/src/dsm/mod.rs +300 -0
  43. risearch-3.0.0a4/src/dsm/model.rs +186 -0
  44. risearch-3.0.0a4/src/dsm/parse.rs +152 -0
  45. risearch-3.0.0a4/src/dsm/tables/mod.rs +39 -0
  46. risearch-3.0.0a4/src/dsm/tables/s95_0.rs +350 -0
  47. risearch-3.0.0a4/src/dsm/tables/s95_25.rs +350 -0
  48. risearch-3.0.0a4/src/dsm/tables/s95_37.rs +350 -0
  49. risearch-3.0.0a4/src/dsm/tables/s95_42.rs +350 -0
  50. risearch-3.0.0a4/src/dsm/tables/s95_50.rs +350 -0
  51. risearch-3.0.0a4/src/dsm/tables/slh04_0.rs +350 -0
  52. risearch-3.0.0a4/src/dsm/tables/slh04_25.rs +350 -0
  53. risearch-3.0.0a4/src/dsm/tables/slh04_37.rs +350 -0
  54. risearch-3.0.0a4/src/dsm/tables/slh04_42.rs +350 -0
  55. risearch-3.0.0a4/src/dsm/tables/slh04_50.rs +350 -0
  56. risearch-3.0.0a4/src/dsm/tables/t04_0.rs +350 -0
  57. risearch-3.0.0a4/src/dsm/tables/t04_25.rs +350 -0
  58. risearch-3.0.0a4/src/dsm/tables/t04_37.rs +350 -0
  59. risearch-3.0.0a4/src/dsm/tables/t04_42.rs +350 -0
  60. risearch-3.0.0a4/src/dsm/tables/t04_50.rs +350 -0
  61. risearch-3.0.0a4/src/error.rs +37 -0
  62. risearch-3.0.0a4/src/fastx/mod.rs +99 -0
  63. risearch-3.0.0a4/src/index/archive.rs +485 -0
  64. risearch-3.0.0a4/src/index/mod.rs +9 -0
  65. risearch-3.0.0a4/src/index/sa.rs +219 -0
  66. risearch-3.0.0a4/src/index/store.rs +263 -0
  67. risearch-3.0.0a4/src/index/view.rs +236 -0
  68. risearch-3.0.0a4/src/lib.rs +95 -0
  69. risearch-3.0.0a4/src/main.rs +11 -0
  70. risearch-3.0.0a4/src/output/format.rs +284 -0
  71. risearch-3.0.0a4/src/output/mod.rs +9 -0
  72. risearch-3.0.0a4/src/output/sink.rs +100 -0
  73. risearch-3.0.0a4/src/output/writer.rs +237 -0
  74. risearch-3.0.0a4/src/proofs.rs +60 -0
  75. risearch-3.0.0a4/src/registry/mod.rs +363 -0
  76. risearch-3.0.0a4/src/search/extension.rs +497 -0
  77. risearch-3.0.0a4/src/search/metamorphic_tests.rs +202 -0
  78. risearch-3.0.0a4/src/search/mod.rs +1292 -0
  79. risearch-3.0.0a4/src/seed/engine.rs +227 -0
  80. risearch-3.0.0a4/src/seed/mod.rs +119 -0
  81. risearch-3.0.0a4/src/seed/parallel_sa.rs +570 -0
  82. risearch-3.0.0a4/src/seed/reference_tests.rs +484 -0
  83. risearch-3.0.0a4/src/seq/mod.rs +11 -0
  84. risearch-3.0.0a4/src/seq/normalize.rs +119 -0
  85. risearch-3.0.0a4/src/seq/sequence.rs +210 -0
  86. risearch-3.0.0a4/src/types.rs +515 -0
risearch-3.0.0a4/CITATION.cff ADDED
@@ -0,0 +1,35 @@
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+ cff-version: 1.2.0
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+ message: "If you use RIsearch, please cite the following references."
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+ title: RIsearch
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+ license: BUSL-1.1
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+ repository-code: "https://github.com/saiden89/risearch"
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+ authors:
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+ - family-names: Roncelli
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+ given-names: Stefano
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+ orcid: "https://orcid.org/0009-0001-4830-202X"
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+ - family-names: Favaro
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+ given-names: Lorenzo
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+ orcid: "https://orcid.org/0009-0002-8879-0555"
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+ - family-names: Anthon
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+ given-names: Christian
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+ orcid: "https://orcid.org/0000-0002-4336-1688"
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+ - family-names: Gorodkin
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+ given-names: Jan
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+ orcid: "https://orcid.org/0000-0001-5823-4000"
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+ preferred-citation:
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+ type: article
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+ title: "RIsearch and RIOT: An integrated, high-performance framework for RNA-RNA interaction and siRNA off-target prediction"
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+ journal: Bioinformatics
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+ authors:
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+ - family-names: Roncelli
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+ given-names: Stefano
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+ orcid: "https://orcid.org/0009-0001-4830-202X"
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+ - family-names: Favaro
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+ given-names: Lorenzo
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+ orcid: "https://orcid.org/0009-0002-8879-0555"
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+ - family-names: Anthon
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+ given-names: Christian
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+ orcid: "https://orcid.org/0000-0002-4336-1688"
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+ - family-names: Gorodkin
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+ given-names: Jan
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+ orcid: "https://orcid.org/0000-0001-5823-4000"