smftools 0.3.0__py3-none-any.whl → 0.3.2__py3-none-any.whl

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Files changed (66) hide show
  1. smftools/_version.py +1 -1
  2. smftools/cli/chimeric_adata.py +1563 -0
  3. smftools/cli/helpers.py +49 -7
  4. smftools/cli/hmm_adata.py +250 -32
  5. smftools/cli/latent_adata.py +773 -0
  6. smftools/cli/load_adata.py +78 -74
  7. smftools/cli/preprocess_adata.py +122 -58
  8. smftools/cli/recipes.py +26 -0
  9. smftools/cli/spatial_adata.py +74 -112
  10. smftools/cli/variant_adata.py +423 -0
  11. smftools/cli_entry.py +52 -4
  12. smftools/config/conversion.yaml +1 -1
  13. smftools/config/deaminase.yaml +3 -0
  14. smftools/config/default.yaml +85 -12
  15. smftools/config/experiment_config.py +146 -1
  16. smftools/constants.py +69 -0
  17. smftools/hmm/HMM.py +88 -0
  18. smftools/hmm/call_hmm_peaks.py +1 -1
  19. smftools/informatics/__init__.py +6 -0
  20. smftools/informatics/bam_functions.py +358 -8
  21. smftools/informatics/binarize_converted_base_identities.py +2 -89
  22. smftools/informatics/converted_BAM_to_adata.py +636 -175
  23. smftools/informatics/h5ad_functions.py +198 -2
  24. smftools/informatics/modkit_extract_to_adata.py +1007 -425
  25. smftools/informatics/sequence_encoding.py +72 -0
  26. smftools/logging_utils.py +21 -2
  27. smftools/metadata.py +1 -1
  28. smftools/plotting/__init__.py +26 -3
  29. smftools/plotting/autocorrelation_plotting.py +22 -4
  30. smftools/plotting/chimeric_plotting.py +1893 -0
  31. smftools/plotting/classifiers.py +28 -14
  32. smftools/plotting/general_plotting.py +62 -1583
  33. smftools/plotting/hmm_plotting.py +1670 -8
  34. smftools/plotting/latent_plotting.py +804 -0
  35. smftools/plotting/plotting_utils.py +243 -0
  36. smftools/plotting/position_stats.py +16 -8
  37. smftools/plotting/preprocess_plotting.py +281 -0
  38. smftools/plotting/qc_plotting.py +8 -3
  39. smftools/plotting/spatial_plotting.py +1134 -0
  40. smftools/plotting/variant_plotting.py +1231 -0
  41. smftools/preprocessing/__init__.py +4 -0
  42. smftools/preprocessing/append_base_context.py +18 -18
  43. smftools/preprocessing/append_mismatch_frequency_sites.py +187 -0
  44. smftools/preprocessing/append_sequence_mismatch_annotations.py +171 -0
  45. smftools/preprocessing/append_variant_call_layer.py +480 -0
  46. smftools/preprocessing/calculate_consensus.py +1 -1
  47. smftools/preprocessing/calculate_read_modification_stats.py +6 -1
  48. smftools/preprocessing/flag_duplicate_reads.py +4 -4
  49. smftools/preprocessing/invert_adata.py +1 -0
  50. smftools/readwrite.py +159 -99
  51. smftools/schema/anndata_schema_v1.yaml +15 -1
  52. smftools/tools/__init__.py +10 -0
  53. smftools/tools/calculate_knn.py +121 -0
  54. smftools/tools/calculate_leiden.py +57 -0
  55. smftools/tools/calculate_nmf.py +130 -0
  56. smftools/tools/calculate_pca.py +180 -0
  57. smftools/tools/calculate_umap.py +79 -80
  58. smftools/tools/position_stats.py +4 -4
  59. smftools/tools/rolling_nn_distance.py +872 -0
  60. smftools/tools/sequence_alignment.py +140 -0
  61. smftools/tools/tensor_factorization.py +217 -0
  62. {smftools-0.3.0.dist-info → smftools-0.3.2.dist-info}/METADATA +9 -5
  63. {smftools-0.3.0.dist-info → smftools-0.3.2.dist-info}/RECORD +66 -45
  64. {smftools-0.3.0.dist-info → smftools-0.3.2.dist-info}/WHEEL +0 -0
  65. {smftools-0.3.0.dist-info → smftools-0.3.2.dist-info}/entry_points.txt +0 -0
  66. {smftools-0.3.0.dist-info → smftools-0.3.2.dist-info}/licenses/LICENSE +0 -0
smftools/_version.py CHANGED
@@ -1,3 +1,3 @@
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  from __future__ import annotations
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- __version__ = "0.3.0"
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+ __version__ = "0.3.2"