biolect 0.0.0.dev1__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.
Files changed (79) hide show
  1. biolect/__init__.py +27 -0
  2. biolect/core/__init__.py +0 -0
  3. biolect/core/definitions/__init__.py +0 -0
  4. biolect/core/dtypes.py +62 -0
  5. biolect/core/errors/__init__.py +26 -0
  6. biolect/core/errors/etypes.py +55 -0
  7. biolect/core/errors/handlers.py +76 -0
  8. biolect/core/errors/monadic.py +0 -0
  9. biolect/core/errors/recovery.py +0 -0
  10. biolect/core/operations.py +0 -0
  11. biolect/core/pipeline.py +0 -0
  12. biolect/core/validation.py +0 -0
  13. biolect/formats/fasta.py +0 -0
  14. biolect/formats/fastq.py +0 -0
  15. biolect/formats/gff.py +0 -0
  16. biolect/formats/parsers/__init__.py +0 -0
  17. biolect/formats/parsers/safe_parsers.py +0 -0
  18. biolect/formats/parsers/validators.py +0 -0
  19. biolect/formats/phylip.py +0 -0
  20. biolect/formats/sambam.py +0 -0
  21. biolect/formats/vcf.py +0 -0
  22. biolect/integrations/__init__.py +0 -0
  23. biolect/integrations/blast.py +0 -0
  24. biolect/integrations/clustal.py +0 -0
  25. biolect/integrations/external.py +0 -0
  26. biolect/integrations/muscle.py +0 -0
  27. biolect/integrations/raxml.py +0 -0
  28. biolect/integrations/safe/__init__.py +0 -0
  29. biolect/integrations/safe/blast_safe.py +0 -0
  30. biolect/integrations/safe/tools_safe.py +0 -0
  31. biolect/operations/__init__.py +26 -0
  32. biolect/operations/alignment/__init__.py +0 -0
  33. biolect/operations/alignment/consensus.py +0 -0
  34. biolect/operations/alignment/multiple.py +0 -0
  35. biolect/operations/alignment/pairwise.py +0 -0
  36. biolect/operations/alignment/safe/__init__.py +0 -0
  37. biolect/operations/alignment/safe/monadic_ops.py +0 -0
  38. biolect/operations/analysis/__init__.py +0 -0
  39. biolect/operations/analysis/clustering.py +0 -0
  40. biolect/operations/analysis/quality.py +0 -0
  41. biolect/operations/analysis/safe/__init__.py +0 -0
  42. biolect/operations/analysis/safe/monadic_ops.py +0 -0
  43. biolect/operations/analysis/statistics.py +0 -0
  44. biolect/operations/analysis/visualization.py +0 -0
  45. biolect/operations/annotation/__init__.py +0 -0
  46. biolect/operations/annotation/comparative.py +0 -0
  47. biolect/operations/annotation/functional.py +0 -0
  48. biolect/operations/annotation/gene_calling.py +0 -0
  49. biolect/operations/annotation/safe/__init__.py +0 -0
  50. biolect/operations/annotation/safe/monadic_ops.py +0 -0
  51. biolect/operations/phylogenetics/__init__.py +0 -0
  52. biolect/operations/phylogenetics/distance.py +0 -0
  53. biolect/operations/phylogenetics/safe/__init__.py +0 -0
  54. biolect/operations/phylogenetics/safe/monadic_ops.py +0 -0
  55. biolect/operations/phylogenetics/trees.py +0 -0
  56. biolect/operations/phylogenetics/visualization.py +0 -0
  57. biolect/operations/sequencing/__init__.py +28 -0
  58. biolect/operations/sequencing/analysis.py +16 -0
  59. biolect/operations/sequencing/encoding.py +193 -0
  60. biolect/operations/sequencing/manipulation.py +0 -0
  61. biolect/operations/sequencing/safe/__init__.py +0 -0
  62. biolect/operations/sequencing/safe/monadic_ops.py +0 -0
  63. biolect/operations/sequencing/search.py +0 -0
  64. biolect/operations/sequencing/translation.py +0 -0
  65. biolect/utilities/__init__.py +0 -0
  66. biolect/utilities/caching.py +0 -0
  67. biolect/utilities/config.py +0 -0
  68. biolect/utilities/memory.py +0 -0
  69. biolect/utilities/parallel.py +0 -0
  70. biolect/utilities/progress.py +0 -0
  71. biolect/visualization/__init__.py +0 -0
  72. biolect/visualization/alignments.py +0 -0
  73. biolect/visualization/genomics.py +0 -0
  74. biolect/visualization/sequences.py +0 -0
  75. biolect/visualization/trees.py +0 -0
  76. biolect-0.0.0.dev1.dist-info/METADATA +40 -0
  77. biolect-0.0.0.dev1.dist-info/RECORD +79 -0
  78. biolect-0.0.0.dev1.dist-info/WHEEL +4 -0
  79. biolect-0.0.0.dev1.dist-info/licenses/LICENSE +661 -0
biolect/utilities/memory.py ADDED
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biolect/utilities/parallel.py ADDED
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biolect/utilities/progress.py ADDED
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biolect/visualization/__init__.py ADDED
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biolect/visualization/alignments.py ADDED
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biolect/visualization/genomics.py ADDED
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biolect/visualization/sequences.py ADDED
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biolect/visualization/trees.py ADDED
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biolect-0.0.0.dev1.dist-info/METADATA ADDED
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+ Metadata-Version: 2.4
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+ Name: biolect
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+ Version: 0.0.0.dev1
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+ Summary: An embedded bioinformatics DSL framework.
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+ Author-email: "K. LeBryce" <k.lebryce@pm.me>
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+ License-File: LICENSE
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+ Requires-Python: >=3.11
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+ Requires-Dist: biopython>=1.85
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+ Requires-Dist: matplotlib>=3.10.3
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+ Requires-Dist: numpy>=2.2.6
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+ Requires-Dist: pandas>=2.2.3
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+ Requires-Dist: polars>=1.30.0
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+ Requires-Dist: python-dotenv>=1.1.0
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+ Requires-Dist: returns>=0.25.0
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+ Requires-Dist: scipy>=1.15.3
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+ Requires-Dist: seaborn>=0.13.2
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+ Requires-Dist: sympy>=1.14.0
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+ Description-Content-Type: text/markdown
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+
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+ # Biolect
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+
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+ `v0.0.0`, "_Adenine_"
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+
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+ ![Python](https://img.shields.io/badge/python-gray?logo=python&logoColor=gold&link=https%3A%2F%2Fwww.python.org%2F)
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+
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+ ![GitHub branch status](https://img.shields.io/github/checks-status/kosmolebryce/biolect/main)
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+
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+ A bioinformatics-oriented DSL framework.
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+
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+ ---
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+
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+ > [!NOTE]
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+ > This project is a work in progress. Because it is in such early stages of
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+ > development, virtually every aspect of its API is subject to change. Use
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+ > at your own risk.
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+
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+
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+ ## Overview
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+
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+ (Coming soon.)
biolect-0.0.0.dev1.dist-info/RECORD ADDED
@@ -0,0 +1,79 @@
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+ biolect/__init__.py,sha256=Yx2GaqtcrCmS39GJgyEid1T-iHm3AahlXrU_D6YEd-w,1453
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+ biolect/core/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/dtypes.py,sha256=10j5tC-dQlfAW0G2W37Hst71xr9HSN42fYGJyR30wK0,1602
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+ biolect/core/operations.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/pipeline.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/validation.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/definitions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/errors/__init__.py,sha256=LCemZwTQx8V7zl8_RD8cEk50pZVXPjVkZVXErZV0K4s,1002
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+ biolect/core/errors/etypes.py,sha256=tVs5fWC9tY_YFfjgIj8wsapRK0uMBcq7UEqu6A7PBwc,1673
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+ biolect/core/errors/handlers.py,sha256=yaYmIZzI3-rz3boWThcI7St14ES5cyanLTfd0Q4eYp0,1957
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+ biolect/core/errors/monadic.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/core/errors/recovery.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/fasta.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/fastq.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/gff.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/phylip.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/sambam.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/vcf.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/parsers/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/formats/parsers/safe_parsers.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
21
+ biolect/formats/parsers/validators.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/blast.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/clustal.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/external.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/muscle.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/raxml.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/integrations/safe/blast_safe.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
30
+ biolect/integrations/safe/tools_safe.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/__init__.py,sha256=scWh3tVkWm7m8uKKNr0hH9t7SOME6YNBCPfy5rFhQ1M,1180
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+ biolect/operations/alignment/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/alignment/consensus.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/alignment/multiple.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/alignment/pairwise.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/alignment/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/alignment/safe/monadic_ops.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/clustering.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/quality.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/statistics.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/visualization.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/analysis/safe/monadic_ops.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/comparative.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/functional.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/gene_calling.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/annotation/safe/monadic_ops.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/distance.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/trees.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/visualization.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/phylogenetics/safe/monadic_ops.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/sequencing/__init__.py,sha256=d3BeoAzZKzAlOEeSCSAGiVQGMdyPCbqEZ7h4h9J0Uus,1646
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+ biolect/operations/sequencing/analysis.py,sha256=w7fj40XGDJ2BXYgA_IM9ct4Cy9xoR0d4P7A2QZqaqp4,434
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+ biolect/operations/sequencing/encoding.py,sha256=KO5GMVMeJShYI_FlrP8GD96mJA4ZxoXYjSun7wGX6RE,6461
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+ biolect/operations/sequencing/manipulation.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/sequencing/search.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/sequencing/translation.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/sequencing/safe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/operations/sequencing/safe/monadic_ops.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/caching.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/config.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/memory.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/parallel.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/utilities/progress.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/visualization/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/visualization/alignments.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/visualization/genomics.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/visualization/sequences.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect/visualization/trees.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ biolect-0.0.0.dev1.dist-info/METADATA,sha256=43RnZJxe3tEC0VocEfCxGFjod2uGSNDn7VbZkIYMJ5U,1054
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+ biolect-0.0.0.dev1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ biolect-0.0.0.dev1.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
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+ biolect-0.0.0.dev1.dist-info/RECORD,,
biolect-0.0.0.dev1.dist-info/WHEEL ADDED
@@ -0,0 +1,4 @@
1
+ Wheel-Version: 1.0
2
+ Generator: hatchling 1.27.0
3
+ Root-Is-Purelib: true
4
+ Tag: py3-none-any