ligase-bio 0.1.0__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 (115) hide show
  1. ligase_bio-0.1.0/Cargo.lock +1006 -0
  2. ligase_bio-0.1.0/Cargo.toml +51 -0
  3. ligase_bio-0.1.0/LICENSE-APACHE +202 -0
  4. ligase_bio-0.1.0/LICENSE-MIT +21 -0
  5. ligase_bio-0.1.0/PKG-INFO +89 -0
  6. ligase_bio-0.1.0/README.md +60 -0
  7. ligase_bio-0.1.0/crates/ligase-core/Cargo.toml +37 -0
  8. ligase_bio-0.1.0/crates/ligase-core/README.md +60 -0
  9. ligase_bio-0.1.0/crates/ligase-core/rulesets/HIVDB_10.2.ruleset +1501 -0
  10. ligase_bio-0.1.0/crates/ligase-core/rulesets/HIVDB_10.2.xml +4408 -0
  11. ligase_bio-0.1.0/crates/ligase-core/rulesets/HIVDB_9.8.ruleset +1417 -0
  12. ligase_bio-0.1.0/crates/ligase-core/rulesets/HIVDB_9.8.xml +4438 -0
  13. ligase_bio-0.1.0/crates/ligase-core/rulesets/PROVENANCE.tsv +12 -0
  14. ligase_bio-0.1.0/crates/ligase-core/rulesets/README.md +75 -0
  15. ligase_bio-0.1.0/crates/ligase-core/src/audit.rs +439 -0
  16. ligase_bio-0.1.0/crates/ligase-core/src/cache.rs +707 -0
  17. ligase_bio-0.1.0/crates/ligase-core/src/canon/alignment.rs +264 -0
  18. ligase_bio-0.1.0/crates/ligase-core/src/canon/fasta.rs +90 -0
  19. ligase_bio-0.1.0/crates/ligase-core/src/canon/intervals.rs +68 -0
  20. ligase_bio-0.1.0/crates/ligase-core/src/canon/mod.rs +442 -0
  21. ligase_bio-0.1.0/crates/ligase-core/src/canon/note.rs +276 -0
  22. ligase_bio-0.1.0/crates/ligase-core/src/canon/reads.rs +57 -0
  23. ligase_bio-0.1.0/crates/ligase-core/src/canon/report.rs +60 -0
  24. ligase_bio-0.1.0/crates/ligase-core/src/canon/variants.rs +277 -0
  25. ligase_bio-0.1.0/crates/ligase-core/src/check.rs +901 -0
  26. ligase_bio-0.1.0/crates/ligase-core/src/dim/mod.rs +479 -0
  27. ligase_bio-0.1.0/crates/ligase-core/src/dim/reference.rs +436 -0
  28. ligase_bio-0.1.0/crates/ligase-core/src/exec.rs +1527 -0
  29. ligase_bio-0.1.0/crates/ligase-core/src/graph.rs +729 -0
  30. ligase_bio-0.1.0/crates/ligase-core/src/hash.rs +182 -0
  31. ligase_bio-0.1.0/crates/ligase-core/src/hivdb/codon.rs +514 -0
  32. ligase_bio-0.1.0/crates/ligase-core/src/hivdb/mod.rs +80 -0
  33. ligase_bio-0.1.0/crates/ligase-core/src/hivdb/report.rs +113 -0
  34. ligase_bio-0.1.0/crates/ligase-core/src/hivdb/ruleset.rs +546 -0
  35. ligase_bio-0.1.0/crates/ligase-core/src/hivdb/score.rs +234 -0
  36. ligase_bio-0.1.0/crates/ligase-core/src/key.rs +170 -0
  37. ligase_bio-0.1.0/crates/ligase-core/src/lib.rs +64 -0
  38. ligase_bio-0.1.0/crates/ligase-core/src/load/alignment.rs +189 -0
  39. ligase_bio-0.1.0/crates/ligase-core/src/load/fasta.rs +129 -0
  40. ligase_bio-0.1.0/crates/ligase-core/src/load/intervals.rs +271 -0
  41. ligase_bio-0.1.0/crates/ligase-core/src/load/mod.rs +144 -0
  42. ligase_bio-0.1.0/crates/ligase-core/src/load/reads.rs +246 -0
  43. ligase_bio-0.1.0/crates/ligase-core/src/load/variants.rs +100 -0
  44. ligase_bio-0.1.0/crates/ligase-core/src/prov/bundle.rs +940 -0
  45. ligase_bio-0.1.0/crates/ligase-core/src/prov/cite.rs +117 -0
  46. ligase_bio-0.1.0/crates/ligase-core/src/prov/methods.rs +759 -0
  47. ligase_bio-0.1.0/crates/ligase-core/src/prov/mod.rs +753 -0
  48. ligase_bio-0.1.0/crates/ligase-core/src/types.rs +177 -0
  49. ligase_bio-0.1.0/crates/ligase-core/tests/audit.rs +422 -0
  50. ligase_bio-0.1.0/crates/ligase-core/tests/canon.rs +824 -0
  51. ligase_bio-0.1.0/crates/ligase-core/tests/check.rs +641 -0
  52. ligase_bio-0.1.0/crates/ligase-core/tests/common/mod.rs +78 -0
  53. ligase_bio-0.1.0/crates/ligase-core/tests/execution.rs +1018 -0
  54. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/generate.py +247 -0
  55. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/hivdb/cases.tsv +744 -0
  56. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/hivdb/expected.tsv +3357 -0
  57. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/reads_ambiguous_1.fastq +8 -0
  58. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/reads_phred33_1.fastq +12 -0
  59. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/reads_phred33_2.fastq +12 -0
  60. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/reads_phred64_1.fastq +12 -0
  61. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.bed +5 -0
  62. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.fasta +4 -0
  63. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.gff +5 -0
  64. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.gtf +3 -0
  65. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.sam +6 -0
  66. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_bare.vcf +6 -0
  67. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_empty.bed +2 -0
  68. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_no_region.gff +5 -0
  69. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_no_rg.sam +5 -0
  70. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_other.fasta +4 -0
  71. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_other.sam +6 -0
  72. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_other.vcf +5 -0
  73. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_prefixed.bed +2 -0
  74. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_prefixed.fasta +4 -0
  75. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_prefixed.sam +6 -0
  76. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_reordered.bed +2 -0
  77. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_reordered.fasta +4 -0
  78. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_reordered.sam +6 -0
  79. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_subset.vcf +5 -0
  80. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_superset.fasta +6 -0
  81. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_swapped_samples.vcf +6 -0
  82. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_two_rg.sam +7 -0
  83. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_two_samples.vcf +6 -0
  84. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_unaligned.sam +4 -0
  85. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_unknown_contig.bed +2 -0
  86. ligase_bio-0.1.0/crates/ligase-core/tests/fixtures/tiny_unknown_contig.sam +6 -0
  87. ligase_bio-0.1.0/crates/ligase-core/tests/graph.rs +1107 -0
  88. ligase_bio-0.1.0/crates/ligase-core/tests/hashing.rs +219 -0
  89. ligase_bio-0.1.0/crates/ligase-core/tests/hivdb_codons.rs +229 -0
  90. ligase_bio-0.1.0/crates/ligase-core/tests/hivdb_scoring.rs +431 -0
  91. ligase_bio-0.1.0/crates/ligase-core/tests/inference.rs +475 -0
  92. ligase_bio-0.1.0/crates/ligase-core/tests/intervals.rs +366 -0
  93. ligase_bio-0.1.0/crates/ligase-core/tests/keys.rs +169 -0
  94. ligase_bio-0.1.0/crates/ligase-core/tests/m1_acceptance.rs +180 -0
  95. ligase_bio-0.1.0/crates/ligase-core/tests/notes.rs +400 -0
  96. ligase_bio-0.1.0/crates/ligase-core/tests/provenance.rs +972 -0
  97. ligase_bio-0.1.0/crates/ligase-core/tests/reference_identity.rs +305 -0
  98. ligase_bio-0.1.0/crates/ligase-core/tests/version.rs +13 -0
  99. ligase_bio-0.1.0/crates/ligase-py/Cargo.toml +23 -0
  100. ligase_bio-0.1.0/crates/ligase-py/src/lib.rs +1021 -0
  101. ligase_bio-0.1.0/pyproject.toml +90 -0
  102. ligase_bio-0.1.0/python/ligase/__init__.py +362 -0
  103. ligase_bio-0.1.0/python/ligase/__main__.py +10 -0
  104. ligase_bio-0.1.0/python/ligase/_core.pyi +228 -0
  105. ligase_bio-0.1.0/python/ligase/audit.py +113 -0
  106. ligase_bio-0.1.0/python/ligase/cli.py +437 -0
  107. ligase_bio-0.1.0/python/ligase/errors.py +155 -0
  108. ligase_bio-0.1.0/python/ligase/graph.py +1120 -0
  109. ligase_bio-0.1.0/python/ligase/hivdb.py +145 -0
  110. ligase_bio-0.1.0/python/ligase/provenance.py +301 -0
  111. ligase_bio-0.1.0/python/ligase/py.typed +0 -0
  112. ligase_bio-0.1.0/python/ligase/recipes.py +117 -0
  113. ligase_bio-0.1.0/python/ligase/run.py +165 -0
  114. ligase_bio-0.1.0/python/ligase/samples.py +90 -0
  115. ligase_bio-0.1.0/python/ligase/types.py +220 -0
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