strandweaver 0.3.0.dev0__tar.gz

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Files changed (86) hide show
  1. strandweaver-0.3.0.dev0/MANIFEST.in +26 -0
  2. strandweaver-0.3.0.dev0/PKG-INFO +1053 -0
  3. strandweaver-0.3.0.dev0/README.md +973 -0
  4. strandweaver-0.3.0.dev0/pyproject.toml +71 -0
  5. strandweaver-0.3.0.dev0/requirements-dev.txt +18 -0
  6. strandweaver-0.3.0.dev0/requirements-gpu.txt +21 -0
  7. strandweaver-0.3.0.dev0/requirements.txt +25 -0
  8. strandweaver-0.3.0.dev0/setup.cfg +4 -0
  9. strandweaver-0.3.0.dev0/setup.py +130 -0
  10. strandweaver-0.3.0.dev0/strandweaver/__init__.py +18 -0
  11. strandweaver-0.3.0.dev0/strandweaver/assembly_core/__init__.py +146 -0
  12. strandweaver-0.3.0.dev0/strandweaver/assembly_core/dbg_engine_module.py +1426 -0
  13. strandweaver-0.3.0.dev0/strandweaver/assembly_core/edgewarden_module.py +3517 -0
  14. strandweaver-0.3.0.dev0/strandweaver/assembly_core/haplotype_detangler_module.py +1482 -0
  15. strandweaver-0.3.0.dev0/strandweaver/assembly_core/illumina_olc_contig_module.py +1283 -0
  16. strandweaver-0.3.0.dev0/strandweaver/assembly_core/pathweaver_module.py +3886 -0
  17. strandweaver-0.3.0.dev0/strandweaver/assembly_core/strandtether_module.py +1525 -0
  18. strandweaver-0.3.0.dev0/strandweaver/assembly_core/string_graph_engine_module.py +744 -0
  19. strandweaver-0.3.0.dev0/strandweaver/assembly_core/svscribe_module.py +1864 -0
  20. strandweaver-0.3.0.dev0/strandweaver/assembly_core/threadcompass_module.py +1557 -0
  21. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/__init__.py +86 -0
  22. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/chromosome_classifier.py +770 -0
  23. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/gap_filler.py +455 -0
  24. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/gene_annotation.py +634 -0
  25. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/graph_cleanup.py +586 -0
  26. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/hic_graph_aligner.py +540 -0
  27. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/iterative_polisher.py +387 -0
  28. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/misassembly_detector.py +1953 -0
  29. strandweaver-0.3.0.dev0/strandweaver/assembly_utils/qv_estimator.py +427 -0
  30. strandweaver-0.3.0.dev0/strandweaver/cli.py +3828 -0
  31. strandweaver-0.3.0.dev0/strandweaver/config/__init__.py +18 -0
  32. strandweaver-0.3.0.dev0/strandweaver/config/defaults.yaml +136 -0
  33. strandweaver-0.3.0.dev0/strandweaver/config/env_ml_training.yml +31 -0
  34. strandweaver-0.3.0.dev0/strandweaver/config/parser.py +267 -0
  35. strandweaver-0.3.0.dev0/strandweaver/config/schema.py +423 -0
  36. strandweaver-0.3.0.dev0/strandweaver/download.py +483 -0
  37. strandweaver-0.3.0.dev0/strandweaver/io_utils/__init__.py +176 -0
  38. strandweaver-0.3.0.dev0/strandweaver/io_utils/assembly_export.py +821 -0
  39. strandweaver-0.3.0.dev0/strandweaver/io_utils/io_core.py +1011 -0
  40. strandweaver-0.3.0.dev0/strandweaver/io_utils/user_input.py +973 -0
  41. strandweaver-0.3.0.dev0/strandweaver/preprocessing/__init__.py +165 -0
  42. strandweaver-0.3.0.dev0/strandweaver/preprocessing/errorsmith_module.py +3352 -0
  43. strandweaver-0.3.0.dev0/strandweaver/preprocessing/kmer_error_features.py +643 -0
  44. strandweaver-0.3.0.dev0/strandweaver/preprocessing/kweaver_module.py +979 -0
  45. strandweaver-0.3.0.dev0/strandweaver/preprocessing/read_classification_utility.py +1130 -0
  46. strandweaver-0.3.0.dev0/strandweaver/preprocessing/read_error_profiling_utility.py +993 -0
  47. strandweaver-0.3.0.dev0/strandweaver/training/__init__.py +56 -0
  48. strandweaver-0.3.0.dev0/strandweaver/training/synthetic_data_generator.py +780 -0
  49. strandweaver-0.3.0.dev0/strandweaver/user_training/__init__.py +88 -0
  50. strandweaver-0.3.0.dev0/strandweaver/user_training/config_based_workflow.py +550 -0
  51. strandweaver-0.3.0.dev0/strandweaver/user_training/generate_sv_dense_data.py +448 -0
  52. strandweaver-0.3.0.dev0/strandweaver/user_training/generate_training_data.py +296 -0
  53. strandweaver-0.3.0.dev0/strandweaver/user_training/graph_training_data.py +1999 -0
  54. strandweaver-0.3.0.dev0/strandweaver/user_training/patch_sv_injection.py +341 -0
  55. strandweaver-0.3.0.dev0/strandweaver/user_training/reextract_sv_features.py +434 -0
  56. strandweaver-0.3.0.dev0/strandweaver/user_training/reextract_sv_only.py +398 -0
  57. strandweaver-0.3.0.dev0/strandweaver/user_training/sv_detection.py +599 -0
  58. strandweaver-0.3.0.dev0/strandweaver/user_training/train_models.py +1567 -0
  59. strandweaver-0.3.0.dev0/strandweaver/user_training/training_config.py +369 -0
  60. strandweaver-0.3.0.dev0/strandweaver/utils/__init__.py +91 -0
  61. strandweaver-0.3.0.dev0/strandweaver/utils/checkpoints.py +192 -0
  62. strandweaver-0.3.0.dev0/strandweaver/utils/hardware_management.py +2938 -0
  63. strandweaver-0.3.0.dev0/strandweaver/utils/pipeline.py +3821 -0
  64. strandweaver-0.3.0.dev0/strandweaver/utils/sequence_utils.py +143 -0
  65. strandweaver-0.3.0.dev0/strandweaver/version.py +16 -0
  66. strandweaver-0.3.0.dev0/strandweaver.egg-info/PKG-INFO +1053 -0
  67. strandweaver-0.3.0.dev0/strandweaver.egg-info/SOURCES.txt +84 -0
  68. strandweaver-0.3.0.dev0/strandweaver.egg-info/dependency_links.txt +1 -0
  69. strandweaver-0.3.0.dev0/strandweaver.egg-info/entry_points.txt +2 -0
  70. strandweaver-0.3.0.dev0/strandweaver.egg-info/not-zip-safe +1 -0
  71. strandweaver-0.3.0.dev0/strandweaver.egg-info/requires.txt +47 -0
  72. strandweaver-0.3.0.dev0/strandweaver.egg-info/top_level.txt +1 -0
  73. strandweaver-0.3.0.dev0/tests/test_bubble_phasing.py +480 -0
  74. strandweaver-0.3.0.dev0/tests/test_cli.py +685 -0
  75. strandweaver-0.3.0.dev0/tests/test_e2e_pipeline.py +396 -0
  76. strandweaver-0.3.0.dev0/tests/test_edgewarden.py +117 -0
  77. strandweaver-0.3.0.dev0/tests/test_graph_training_data.py +598 -0
  78. strandweaver-0.3.0.dev0/tests/test_integration.py +110 -0
  79. strandweaver-0.3.0.dev0/tests/test_kweaver.py +75 -0
  80. strandweaver-0.3.0.dev0/tests/test_polisher_gap_filler.py +372 -0
  81. strandweaver-0.3.0.dev0/tests/test_qv_estimator.py +312 -0
  82. strandweaver-0.3.0.dev0/tests/test_read_classification.py +93 -0
  83. strandweaver-0.3.0.dev0/tests/test_sequence_utils.py +135 -0
  84. strandweaver-0.3.0.dev0/tests/test_train_models.py +364 -0
  85. strandweaver-0.3.0.dev0/tests/test_training_config.py +396 -0
  86. strandweaver-0.3.0.dev0/tests/test_ul_router.py +213 -0
strandweaver-0.3.0.dev0/MANIFEST.in ADDED
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+ # ═══════════════════════════════════════════════════════════════════════
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+ # StrandWeaver — MANIFEST.in
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+ # ═══════════════════════════════════════════════════════════════════════
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+ # Controls which files are included in the source distribution (sdist).
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+ # The wheel only includes what setup.py / find_packages() selects.
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+ # ═══════════════════════════════════════════════════════════════════════
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+
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+ # Include metadata and config
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+ include LICENSE*
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+ include README.md
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+ include CHANGELOG.md
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+ include pyproject.toml
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+ include requirements*.txt
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+ include setup.py
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+
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+ # Include package config YAMLs
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+ recursive-include strandweaver/config *.yaml *.yml
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+
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+ # Exclude large assets (fetched on demand via `strandweaver download`)
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+ prune trained_models
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+ prune nextflow
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+ prune training_data
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+ prune release_assets
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+ prune training_runs
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+ prune benchmarks
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+ prune scripts