smftools 0.2.4__py3-none-any.whl → 0.3.0__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 (181) hide show
  1. smftools/__init__.py +43 -13
  2. smftools/_settings.py +6 -6
  3. smftools/_version.py +3 -1
  4. smftools/cli/__init__.py +1 -0
  5. smftools/cli/archived/cli_flows.py +2 -0
  6. smftools/cli/helpers.py +9 -1
  7. smftools/cli/hmm_adata.py +905 -242
  8. smftools/cli/load_adata.py +432 -280
  9. smftools/cli/preprocess_adata.py +287 -171
  10. smftools/cli/spatial_adata.py +141 -53
  11. smftools/cli_entry.py +119 -178
  12. smftools/config/__init__.py +3 -1
  13. smftools/config/conversion.yaml +5 -1
  14. smftools/config/deaminase.yaml +1 -1
  15. smftools/config/default.yaml +26 -18
  16. smftools/config/direct.yaml +8 -3
  17. smftools/config/discover_input_files.py +19 -5
  18. smftools/config/experiment_config.py +511 -276
  19. smftools/constants.py +37 -0
  20. smftools/datasets/__init__.py +4 -8
  21. smftools/datasets/datasets.py +32 -18
  22. smftools/hmm/HMM.py +2133 -1428
  23. smftools/hmm/__init__.py +24 -14
  24. smftools/hmm/archived/apply_hmm_batched.py +2 -0
  25. smftools/hmm/archived/calculate_distances.py +2 -0
  26. smftools/hmm/archived/call_hmm_peaks.py +18 -1
  27. smftools/hmm/archived/train_hmm.py +2 -0
  28. smftools/hmm/call_hmm_peaks.py +176 -193
  29. smftools/hmm/display_hmm.py +23 -7
  30. smftools/hmm/hmm_readwrite.py +20 -6
  31. smftools/hmm/nucleosome_hmm_refinement.py +104 -14
  32. smftools/informatics/__init__.py +55 -13
  33. smftools/informatics/archived/bam_conversion.py +2 -0
  34. smftools/informatics/archived/bam_direct.py +2 -0
  35. smftools/informatics/archived/basecall_pod5s.py +2 -0
  36. smftools/informatics/archived/basecalls_to_adata.py +2 -0
  37. smftools/informatics/archived/conversion_smf.py +2 -0
  38. smftools/informatics/archived/deaminase_smf.py +1 -0
  39. smftools/informatics/archived/direct_smf.py +2 -0
  40. smftools/informatics/archived/fast5_to_pod5.py +2 -0
  41. smftools/informatics/archived/helpers/archived/__init__.py +2 -0
  42. smftools/informatics/archived/helpers/archived/align_and_sort_BAM.py +16 -1
  43. smftools/informatics/archived/helpers/archived/aligned_BAM_to_bed.py +2 -0
  44. smftools/informatics/archived/helpers/archived/bam_qc.py +14 -1
  45. smftools/informatics/archived/helpers/archived/bed_to_bigwig.py +2 -0
  46. smftools/informatics/archived/helpers/archived/canoncall.py +2 -0
  47. smftools/informatics/archived/helpers/archived/concatenate_fastqs_to_bam.py +8 -1
  48. smftools/informatics/archived/helpers/archived/converted_BAM_to_adata.py +2 -0
  49. smftools/informatics/archived/helpers/archived/count_aligned_reads.py +2 -0
  50. smftools/informatics/archived/helpers/archived/demux_and_index_BAM.py +2 -0
  51. smftools/informatics/archived/helpers/archived/extract_base_identities.py +2 -0
  52. smftools/informatics/archived/helpers/archived/extract_mods.py +2 -0
  53. smftools/informatics/archived/helpers/archived/extract_read_features_from_bam.py +2 -0
  54. smftools/informatics/archived/helpers/archived/extract_read_lengths_from_bed.py +2 -0
  55. smftools/informatics/archived/helpers/archived/extract_readnames_from_BAM.py +2 -0
  56. smftools/informatics/archived/helpers/archived/find_conversion_sites.py +2 -0
  57. smftools/informatics/archived/helpers/archived/generate_converted_FASTA.py +2 -0
  58. smftools/informatics/archived/helpers/archived/get_chromosome_lengths.py +2 -0
  59. smftools/informatics/archived/helpers/archived/get_native_references.py +2 -0
  60. smftools/informatics/archived/helpers/archived/index_fasta.py +2 -0
  61. smftools/informatics/archived/helpers/archived/informatics.py +2 -0
  62. smftools/informatics/archived/helpers/archived/load_adata.py +5 -3
  63. smftools/informatics/archived/helpers/archived/make_modbed.py +2 -0
  64. smftools/informatics/archived/helpers/archived/modQC.py +2 -0
  65. smftools/informatics/archived/helpers/archived/modcall.py +2 -0
  66. smftools/informatics/archived/helpers/archived/ohe_batching.py +2 -0
  67. smftools/informatics/archived/helpers/archived/ohe_layers_decode.py +2 -0
  68. smftools/informatics/archived/helpers/archived/one_hot_decode.py +2 -0
  69. smftools/informatics/archived/helpers/archived/one_hot_encode.py +2 -0
  70. smftools/informatics/archived/helpers/archived/plot_bed_histograms.py +5 -1
  71. smftools/informatics/archived/helpers/archived/separate_bam_by_bc.py +2 -0
  72. smftools/informatics/archived/helpers/archived/split_and_index_BAM.py +2 -0
  73. smftools/informatics/archived/print_bam_query_seq.py +9 -1
  74. smftools/informatics/archived/subsample_fasta_from_bed.py +2 -0
  75. smftools/informatics/archived/subsample_pod5.py +2 -0
  76. smftools/informatics/bam_functions.py +1059 -269
  77. smftools/informatics/basecalling.py +53 -9
  78. smftools/informatics/bed_functions.py +357 -114
  79. smftools/informatics/binarize_converted_base_identities.py +21 -7
  80. smftools/informatics/complement_base_list.py +9 -6
  81. smftools/informatics/converted_BAM_to_adata.py +324 -137
  82. smftools/informatics/fasta_functions.py +251 -89
  83. smftools/informatics/h5ad_functions.py +202 -30
  84. smftools/informatics/modkit_extract_to_adata.py +623 -274
  85. smftools/informatics/modkit_functions.py +87 -44
  86. smftools/informatics/ohe.py +46 -21
  87. smftools/informatics/pod5_functions.py +114 -74
  88. smftools/informatics/run_multiqc.py +20 -14
  89. smftools/logging_utils.py +51 -0
  90. smftools/machine_learning/__init__.py +23 -12
  91. smftools/machine_learning/data/__init__.py +2 -0
  92. smftools/machine_learning/data/anndata_data_module.py +157 -50
  93. smftools/machine_learning/data/preprocessing.py +4 -1
  94. smftools/machine_learning/evaluation/__init__.py +3 -1
  95. smftools/machine_learning/evaluation/eval_utils.py +13 -14
  96. smftools/machine_learning/evaluation/evaluators.py +52 -34
  97. smftools/machine_learning/inference/__init__.py +3 -1
  98. smftools/machine_learning/inference/inference_utils.py +9 -4
  99. smftools/machine_learning/inference/lightning_inference.py +14 -13
  100. smftools/machine_learning/inference/sklearn_inference.py +8 -8
  101. smftools/machine_learning/inference/sliding_window_inference.py +37 -25
  102. smftools/machine_learning/models/__init__.py +12 -5
  103. smftools/machine_learning/models/base.py +34 -43
  104. smftools/machine_learning/models/cnn.py +22 -13
  105. smftools/machine_learning/models/lightning_base.py +78 -42
  106. smftools/machine_learning/models/mlp.py +18 -5
  107. smftools/machine_learning/models/positional.py +10 -4
  108. smftools/machine_learning/models/rnn.py +8 -3
  109. smftools/machine_learning/models/sklearn_models.py +46 -24
  110. smftools/machine_learning/models/transformer.py +75 -55
  111. smftools/machine_learning/models/wrappers.py +8 -3
  112. smftools/machine_learning/training/__init__.py +4 -2
  113. smftools/machine_learning/training/train_lightning_model.py +42 -23
  114. smftools/machine_learning/training/train_sklearn_model.py +11 -15
  115. smftools/machine_learning/utils/__init__.py +3 -1
  116. smftools/machine_learning/utils/device.py +12 -5
  117. smftools/machine_learning/utils/grl.py +8 -2
  118. smftools/metadata.py +443 -0
  119. smftools/optional_imports.py +31 -0
  120. smftools/plotting/__init__.py +32 -17
  121. smftools/plotting/autocorrelation_plotting.py +153 -48
  122. smftools/plotting/classifiers.py +175 -73
  123. smftools/plotting/general_plotting.py +350 -168
  124. smftools/plotting/hmm_plotting.py +53 -14
  125. smftools/plotting/position_stats.py +155 -87
  126. smftools/plotting/qc_plotting.py +25 -12
  127. smftools/preprocessing/__init__.py +35 -37
  128. smftools/preprocessing/append_base_context.py +105 -79
  129. smftools/preprocessing/append_binary_layer_by_base_context.py +75 -37
  130. smftools/preprocessing/{archives → archived}/add_read_length_and_mapping_qc.py +2 -0
  131. smftools/preprocessing/{archives → archived}/calculate_complexity.py +5 -1
  132. smftools/preprocessing/{archives → archived}/mark_duplicates.py +2 -0
  133. smftools/preprocessing/{archives → archived}/preprocessing.py +10 -6
  134. smftools/preprocessing/{archives → archived}/remove_duplicates.py +2 -0
  135. smftools/preprocessing/binarize.py +21 -4
  136. smftools/preprocessing/binarize_on_Youden.py +127 -31
  137. smftools/preprocessing/binary_layers_to_ohe.py +18 -11
  138. smftools/preprocessing/calculate_complexity_II.py +89 -59
  139. smftools/preprocessing/calculate_consensus.py +28 -19
  140. smftools/preprocessing/calculate_coverage.py +44 -22
  141. smftools/preprocessing/calculate_pairwise_differences.py +4 -1
  142. smftools/preprocessing/calculate_pairwise_hamming_distances.py +7 -3
  143. smftools/preprocessing/calculate_position_Youden.py +110 -55
  144. smftools/preprocessing/calculate_read_length_stats.py +52 -23
  145. smftools/preprocessing/calculate_read_modification_stats.py +91 -57
  146. smftools/preprocessing/clean_NaN.py +38 -28
  147. smftools/preprocessing/filter_adata_by_nan_proportion.py +24 -12
  148. smftools/preprocessing/filter_reads_on_length_quality_mapping.py +72 -37
  149. smftools/preprocessing/filter_reads_on_modification_thresholds.py +183 -73
  150. smftools/preprocessing/flag_duplicate_reads.py +708 -303
  151. smftools/preprocessing/invert_adata.py +26 -11
  152. smftools/preprocessing/load_sample_sheet.py +40 -22
  153. smftools/preprocessing/make_dirs.py +9 -3
  154. smftools/preprocessing/min_non_diagonal.py +4 -1
  155. smftools/preprocessing/recipes.py +58 -23
  156. smftools/preprocessing/reindex_references_adata.py +93 -27
  157. smftools/preprocessing/subsample_adata.py +33 -16
  158. smftools/readwrite.py +264 -109
  159. smftools/schema/__init__.py +11 -0
  160. smftools/schema/anndata_schema_v1.yaml +227 -0
  161. smftools/tools/__init__.py +25 -18
  162. smftools/tools/archived/apply_hmm.py +2 -0
  163. smftools/tools/archived/classifiers.py +165 -0
  164. smftools/tools/archived/classify_methylated_features.py +2 -0
  165. smftools/tools/archived/classify_non_methylated_features.py +2 -0
  166. smftools/tools/archived/subset_adata_v1.py +12 -1
  167. smftools/tools/archived/subset_adata_v2.py +14 -1
  168. smftools/tools/calculate_umap.py +56 -15
  169. smftools/tools/cluster_adata_on_methylation.py +122 -47
  170. smftools/tools/general_tools.py +70 -25
  171. smftools/tools/position_stats.py +220 -99
  172. smftools/tools/read_stats.py +50 -29
  173. smftools/tools/spatial_autocorrelation.py +365 -192
  174. smftools/tools/subset_adata.py +23 -21
  175. smftools-0.3.0.dist-info/METADATA +147 -0
  176. smftools-0.3.0.dist-info/RECORD +182 -0
  177. smftools-0.2.4.dist-info/METADATA +0 -141
  178. smftools-0.2.4.dist-info/RECORD +0 -176
  179. {smftools-0.2.4.dist-info → smftools-0.3.0.dist-info}/WHEEL +0 -0
  180. {smftools-0.2.4.dist-info → smftools-0.3.0.dist-info}/entry_points.txt +0 -0
  181. {smftools-0.2.4.dist-info → smftools-0.3.0.dist-info}/licenses/LICENSE +0 -0
smftools-0.2.4.dist-info/RECORD DELETED
@@ -1,176 +0,0 @@
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