dnakit 0.1.0.dev0__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 (210) hide show
  1. dnakit/__init__.py +108 -0
  2. dnakit/_version.py +5 -0
  3. dnakit/alignment/__init__.py +6 -0
  4. dnakit/alignment/pairwise.py +512 -0
  5. dnakit/alignment/results.py +188 -0
  6. dnakit/backends/__init__.py +80 -0
  7. dnakit/backends/external.py +517 -0
  8. dnakit/backends/registry.py +207 -0
  9. dnakit/batch.py +452 -0
  10. dnakit/cache/__init__.py +5 -0
  11. dnakit/cache/store.py +424 -0
  12. dnakit/chunking.py +920 -0
  13. dnakit/cli/__init__.py +5 -0
  14. dnakit/cli/__main__.py +6 -0
  15. dnakit/cli/app.py +814 -0
  16. dnakit/cli/workflow.py +94 -0
  17. dnakit/config/__init__.py +5 -0
  18. dnakit/config/loader.py +381 -0
  19. dnakit/core/__init__.py +80 -0
  20. dnakit/core/_json.py +206 -0
  21. dnakit/core/backend_info.py +70 -0
  22. dnakit/core/collection.py +163 -0
  23. dnakit/core/coordinates.py +295 -0
  24. dnakit/core/enums.py +95 -0
  25. dnakit/core/facade.py +719 -0
  26. dnakit/core/feature.py +90 -0
  27. dnakit/core/gap.py +82 -0
  28. dnakit/core/issues.py +62 -0
  29. dnakit/core/provenance.py +305 -0
  30. dnakit/core/record.py +161 -0
  31. dnakit/core/results.py +134 -0
  32. dnakit/core/sequence.py +327 -0
  33. dnakit/datasets/__init__.py +100 -0
  34. dnakit/datasets/_advanced_shared.py +198 -0
  35. dnakit/datasets/_metadata.py +33 -0
  36. dnakit/datasets/advanced_deduplicate.py +183 -0
  37. dnakit/datasets/advanced_split.py +302 -0
  38. dnakit/datasets/clustering.py +286 -0
  39. dnakit/datasets/config.py +531 -0
  40. dnakit/datasets/deduplicate.py +303 -0
  41. dnakit/datasets/evaluation.py +244 -0
  42. dnakit/datasets/filter.py +135 -0
  43. dnakit/datasets/neural_clustering.py +221 -0
  44. dnakit/datasets/results.py +520 -0
  45. dnakit/datasets/split.py +450 -0
  46. dnakit/descriptors/__init__.py +102 -0
  47. dnakit/descriptors/_dinucleotide.py +345 -0
  48. dnakit/descriptors/_shared.py +180 -0
  49. dnakit/descriptors/all.py +917 -0
  50. dnakit/descriptors/basic.py +193 -0
  51. dnakit/descriptors/codon.py +195 -0
  52. dnakit/descriptors/complexity.py +201 -0
  53. dnakit/descriptors/entropy.py +101 -0
  54. dnakit/descriptors/homopolymer.py +105 -0
  55. dnakit/descriptors/kmer.py +88 -0
  56. dnakit/descriptors/results.py +286 -0
  57. dnakit/descriptors/schema.py +414 -0
  58. dnakit/descriptors/window.py +203 -0
  59. dnakit/download/__init__.py +54 -0
  60. dnakit/download/catalogs.py +166 -0
  61. dnakit/download/ena.py +131 -0
  62. dnakit/download/encode.py +103 -0
  63. dnakit/download/files.py +469 -0
  64. dnakit/download/indexes.py +233 -0
  65. dnakit/download/metadata.py +164 -0
  66. dnakit/download/models.py +227 -0
  67. dnakit/download/ncbi.py +333 -0
  68. dnakit/download/sequence.py +133 -0
  69. dnakit/download/ucsc.py +99 -0
  70. dnakit/evaluation/__init__.py +81 -0
  71. dnakit/evaluation/_shared.py +288 -0
  72. dnakit/evaluation/collection.py +270 -0
  73. dnakit/evaluation/config.py +591 -0
  74. dnakit/evaluation/distribution.py +287 -0
  75. dnakit/evaluation/frechet.py +223 -0
  76. dnakit/evaluation/generative.py +381 -0
  77. dnakit/evaluation/reference.py +409 -0
  78. dnakit/evaluation/results.py +137 -0
  79. dnakit/evaluation/scorecard.py +211 -0
  80. dnakit/evaluation/sequence.py +403 -0
  81. dnakit/evaluation/synthesis.py +249 -0
  82. dnakit/exceptions.py +189 -0
  83. dnakit/fingerprints/__init__.py +109 -0
  84. dnakit/fingerprints/_shared.py +116 -0
  85. dnakit/fingerprints/advanced.py +829 -0
  86. dnakit/fingerprints/bit.py +229 -0
  87. dnakit/fingerprints/encoding.py +351 -0
  88. dnakit/fingerprints/kmer.py +170 -0
  89. dnakit/fingerprints/results.py +531 -0
  90. dnakit/fingerprints/sketch.py +246 -0
  91. dnakit/io/__init__.py +112 -0
  92. dnakit/io/_advanced_common.py +105 -0
  93. dnakit/io/_formats.py +994 -0
  94. dnakit/io/annotations.py +1179 -0
  95. dnakit/io/api.py +759 -0
  96. dnakit/io/config.py +315 -0
  97. dnakit/io/genbank.py +523 -0
  98. dnakit/io/indexed.py +1146 -0
  99. dnakit/io/metadata.py +452 -0
  100. dnakit/io/parquet.py +56 -0
  101. dnakit/io/results.py +131 -0
  102. dnakit/io/source.py +138 -0
  103. dnakit/io/tables.py +1237 -0
  104. dnakit/molbio/__init__.py +101 -0
  105. dnakit/molbio/_shared.py +266 -0
  106. dnakit/molbio/assembly.py +279 -0
  107. dnakit/molbio/crispr.py +181 -0
  108. dnakit/molbio/optimization.py +897 -0
  109. dnakit/molbio/primer3_design.py +667 -0
  110. dnakit/molbio/primers.py +899 -0
  111. dnakit/molbio/restriction.py +573 -0
  112. dnakit/molbio/results.py +583 -0
  113. dnakit/ops/__init__.py +588 -0
  114. dnakit/ops/_common.py +201 -0
  115. dnakit/ops/circular.py +193 -0
  116. dnakit/ops/concat.py +204 -0
  117. dnakit/ops/direction.py +27 -0
  118. dnakit/ops/edit.py +443 -0
  119. dnakit/ops/evolution.py +991 -0
  120. dnakit/ops/mutation.py +151 -0
  121. dnakit/ops/records.py +1012 -0
  122. dnakit/ops/translation.py +257 -0
  123. dnakit/patterns/__init__.py +81 -0
  124. dnakit/patterns/_shared.py +282 -0
  125. dnakit/patterns/coding.py +360 -0
  126. dnakit/patterns/crispr.py +337 -0
  127. dnakit/patterns/motif.py +721 -0
  128. dnakit/patterns/regions.py +341 -0
  129. dnakit/patterns/repeats.py +480 -0
  130. dnakit/patterns/restriction.py +281 -0
  131. dnakit/patterns/results.py +411 -0
  132. dnakit/py.typed +1 -0
  133. dnakit/references/__init__.py +27 -0
  134. dnakit/references/models.py +155 -0
  135. dnakit/references/ncbi.py +785 -0
  136. dnakit/representations/__init__.py +29 -0
  137. dnakit/representations/backends.py +928 -0
  138. dnakit/representations/checkpoints.py +356 -0
  139. dnakit/representations/extraction.py +220 -0
  140. dnakit/representations/models.py +395 -0
  141. dnakit/representations/results.py +79 -0
  142. dnakit/search/__init__.py +132 -0
  143. dnakit/search/_http.py +271 -0
  144. dnakit/search/_shared.py +108 -0
  145. dnakit/search/blast.py +516 -0
  146. dnakit/search/ena.py +245 -0
  147. dnakit/search/encode.py +102 -0
  148. dnakit/search/ensembl.py +874 -0
  149. dnakit/search/models.py +159 -0
  150. dnakit/search/ncbi.py +756 -0
  151. dnakit/search/ucsc.py +388 -0
  152. dnakit/secondary_structure/__init__.py +38 -0
  153. dnakit/secondary_structure/dotbracket.py +410 -0
  154. dnakit/secondary_structure/nupack.py +589 -0
  155. dnakit/secondary_structure/results.py +142 -0
  156. dnakit/similarity/__init__.py +125 -0
  157. dnakit/similarity/_shared.py +152 -0
  158. dnakit/similarity/approximate.py +258 -0
  159. dnakit/similarity/compare.py +162 -0
  160. dnakit/similarity/dashing.py +936 -0
  161. dnakit/similarity/distance.py +279 -0
  162. dnakit/similarity/index.py +365 -0
  163. dnakit/similarity/matrix.py +254 -0
  164. dnakit/similarity/results.py +676 -0
  165. dnakit/similarity/search.py +286 -0
  166. dnakit/similarity/sketch.py +96 -0
  167. dnakit/similarity/vector.py +662 -0
  168. dnakit/standardize/__init__.py +77 -0
  169. dnakit/standardize/_shared.py +100 -0
  170. dnakit/standardize/config.py +411 -0
  171. dnakit/standardize/gaps.py +1060 -0
  172. dnakit/standardize/normalize.py +565 -0
  173. dnakit/standardize/results.py +247 -0
  174. dnakit/standardize/validate.py +487 -0
  175. dnakit/structure3d/__init__.py +47 -0
  176. dnakit/structure3d/_shared.py +47 -0
  177. dnakit/structure3d/geometry.py +773 -0
  178. dnakit/structure3d/pdb.py +253 -0
  179. dnakit/structure3d/results.py +233 -0
  180. dnakit/structure3d/threedna.py +174 -0
  181. dnakit/thermodynamics/__init__.py +112 -0
  182. dnakit/thermodynamics/_shared.py +92 -0
  183. dnakit/thermodynamics/backends.py +653 -0
  184. dnakit/thermodynamics/calculations.py +837 -0
  185. dnakit/thermodynamics/config.py +175 -0
  186. dnakit/thermodynamics/equilibrium.py +340 -0
  187. dnakit/thermodynamics/optics.py +385 -0
  188. dnakit/thermodynamics/parameters.py +79 -0
  189. dnakit/thermodynamics/results.py +445 -0
  190. dnakit/visualization/__init__.py +43 -0
  191. dnakit/visualization/_svg.py +185 -0
  192. dnakit/visualization/advanced.py +314 -0
  193. dnakit/visualization/config.py +255 -0
  194. dnakit/visualization/export.py +349 -0
  195. dnakit/visualization/matrix.py +279 -0
  196. dnakit/visualization/report.py +431 -0
  197. dnakit/visualization/results.py +236 -0
  198. dnakit/visualization/sequence.py +459 -0
  199. dnakit/workflows/__init__.py +45 -0
  200. dnakit/workflows/manifest.py +365 -0
  201. dnakit/workflows/runner.py +1548 -0
  202. dnakit/workflows/schema.py +898 -0
  203. dnakit-0.1.0.dev0.dist-info/METADATA +126 -0
  204. dnakit-0.1.0.dev0.dist-info/RECORD +210 -0
  205. dnakit-0.1.0.dev0.dist-info/WHEEL +5 -0
  206. dnakit-0.1.0.dev0.dist-info/entry_points.txt +2 -0
  207. dnakit-0.1.0.dev0.dist-info/licenses/DISCLAIMER.md +26 -0
  208. dnakit-0.1.0.dev0.dist-info/licenses/LICENSE +21 -0
  209. dnakit-0.1.0.dev0.dist-info/licenses/THIRD_PARTY_NOTICES.md +73 -0
  210. dnakit-0.1.0.dev0.dist-info/top_level.txt +1 -0
dnakit/cli/__init__.py ADDED
@@ -0,0 +1,5 @@
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+ """Command-line interface for DNAKit."""
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+
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+ from dnakit.cli.app import app, run
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+
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+ __all__ = ["app", "run"]
dnakit/cli/__main__.py ADDED
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+ """Allow ``python -m dnakit.cli`` execution."""
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+
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+ from dnakit.cli.app import run
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+
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+ if __name__ == "__main__":
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+ run()