smftools 0.2.1__py3-none-any.whl → 0.2.3__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 (96) hide show
  1. smftools/__init__.py +2 -6
  2. smftools/_version.py +1 -1
  3. smftools/cli/__init__.py +0 -0
  4. smftools/cli/cli_flows.py +94 -0
  5. smftools/cli/hmm_adata.py +338 -0
  6. smftools/cli/load_adata.py +577 -0
  7. smftools/cli/preprocess_adata.py +363 -0
  8. smftools/cli/spatial_adata.py +564 -0
  9. smftools/cli_entry.py +435 -0
  10. smftools/config/conversion.yaml +11 -6
  11. smftools/config/deaminase.yaml +12 -7
  12. smftools/config/default.yaml +36 -25
  13. smftools/config/direct.yaml +25 -1
  14. smftools/config/discover_input_files.py +115 -0
  15. smftools/config/experiment_config.py +109 -12
  16. smftools/informatics/__init__.py +13 -7
  17. smftools/informatics/archived/fast5_to_pod5.py +43 -0
  18. smftools/informatics/archived/helpers/archived/__init__.py +71 -0
  19. smftools/informatics/archived/helpers/archived/align_and_sort_BAM.py +126 -0
  20. smftools/informatics/{helpers → archived/helpers/archived}/aligned_BAM_to_bed.py +6 -4
  21. smftools/informatics/archived/helpers/archived/bam_qc.py +213 -0
  22. smftools/informatics/archived/helpers/archived/bed_to_bigwig.py +90 -0
  23. smftools/informatics/archived/helpers/archived/concatenate_fastqs_to_bam.py +259 -0
  24. smftools/informatics/{helpers → archived/helpers/archived}/count_aligned_reads.py +2 -2
  25. smftools/informatics/{helpers → archived/helpers/archived}/demux_and_index_BAM.py +8 -10
  26. smftools/informatics/{helpers → archived/helpers/archived}/extract_base_identities.py +1 -1
  27. smftools/informatics/{helpers → archived/helpers/archived}/extract_mods.py +15 -13
  28. smftools/informatics/{helpers → archived/helpers/archived}/generate_converted_FASTA.py +2 -0
  29. smftools/informatics/{helpers → archived/helpers/archived}/get_chromosome_lengths.py +9 -8
  30. smftools/informatics/archived/helpers/archived/index_fasta.py +24 -0
  31. smftools/informatics/{helpers → archived/helpers/archived}/make_modbed.py +1 -2
  32. smftools/informatics/{helpers → archived/helpers/archived}/modQC.py +2 -2
  33. smftools/informatics/{helpers → archived/helpers/archived}/plot_bed_histograms.py +0 -19
  34. smftools/informatics/{helpers → archived/helpers/archived}/separate_bam_by_bc.py +6 -5
  35. smftools/informatics/{helpers → archived/helpers/archived}/split_and_index_BAM.py +7 -7
  36. smftools/informatics/archived/subsample_fasta_from_bed.py +49 -0
  37. smftools/informatics/bam_functions.py +812 -0
  38. smftools/informatics/basecalling.py +67 -0
  39. smftools/informatics/bed_functions.py +366 -0
  40. smftools/informatics/{helpers/converted_BAM_to_adata_II.py → converted_BAM_to_adata.py} +42 -30
  41. smftools/informatics/fasta_functions.py +255 -0
  42. smftools/informatics/h5ad_functions.py +197 -0
  43. smftools/informatics/{helpers/modkit_extract_to_adata.py → modkit_extract_to_adata.py} +142 -59
  44. smftools/informatics/modkit_functions.py +129 -0
  45. smftools/informatics/ohe.py +160 -0
  46. smftools/informatics/pod5_functions.py +224 -0
  47. smftools/informatics/{helpers/run_multiqc.py → run_multiqc.py} +5 -2
  48. smftools/plotting/autocorrelation_plotting.py +1 -3
  49. smftools/plotting/general_plotting.py +1037 -362
  50. smftools/preprocessing/__init__.py +2 -0
  51. smftools/preprocessing/append_base_context.py +3 -3
  52. smftools/preprocessing/append_binary_layer_by_base_context.py +4 -4
  53. smftools/preprocessing/binarize.py +17 -0
  54. smftools/preprocessing/binarize_on_Youden.py +2 -2
  55. smftools/preprocessing/calculate_position_Youden.py +1 -1
  56. smftools/preprocessing/calculate_read_modification_stats.py +1 -1
  57. smftools/preprocessing/filter_reads_on_modification_thresholds.py +19 -19
  58. smftools/preprocessing/flag_duplicate_reads.py +1 -1
  59. smftools/readwrite.py +266 -140
  60. {smftools-0.2.1.dist-info → smftools-0.2.3.dist-info}/METADATA +10 -9
  61. {smftools-0.2.1.dist-info → smftools-0.2.3.dist-info}/RECORD +82 -70
  62. smftools-0.2.3.dist-info/entry_points.txt +2 -0
  63. smftools/cli.py +0 -184
  64. smftools/informatics/fast5_to_pod5.py +0 -24
  65. smftools/informatics/helpers/__init__.py +0 -73
  66. smftools/informatics/helpers/align_and_sort_BAM.py +0 -86
  67. smftools/informatics/helpers/bam_qc.py +0 -66
  68. smftools/informatics/helpers/bed_to_bigwig.py +0 -39
  69. smftools/informatics/helpers/concatenate_fastqs_to_bam.py +0 -378
  70. smftools/informatics/helpers/discover_input_files.py +0 -100
  71. smftools/informatics/helpers/index_fasta.py +0 -12
  72. smftools/informatics/helpers/make_dirs.py +0 -21
  73. smftools/informatics/readwrite.py +0 -106
  74. smftools/informatics/subsample_fasta_from_bed.py +0 -47
  75. smftools/load_adata.py +0 -1346
  76. smftools-0.2.1.dist-info/entry_points.txt +0 -2
  77. /smftools/informatics/{basecall_pod5s.py → archived/basecall_pod5s.py} +0 -0
  78. /smftools/informatics/{helpers → archived/helpers/archived}/canoncall.py +0 -0
  79. /smftools/informatics/{helpers → archived/helpers/archived}/converted_BAM_to_adata.py +0 -0
  80. /smftools/informatics/{helpers → archived/helpers/archived}/extract_read_features_from_bam.py +0 -0
  81. /smftools/informatics/{helpers → archived/helpers/archived}/extract_read_lengths_from_bed.py +0 -0
  82. /smftools/informatics/{helpers → archived/helpers/archived}/extract_readnames_from_BAM.py +0 -0
  83. /smftools/informatics/{helpers → archived/helpers/archived}/find_conversion_sites.py +0 -0
  84. /smftools/informatics/{helpers → archived/helpers/archived}/get_native_references.py +0 -0
  85. /smftools/informatics/{helpers → archived/helpers}/archived/informatics.py +0 -0
  86. /smftools/informatics/{helpers → archived/helpers}/archived/load_adata.py +0 -0
  87. /smftools/informatics/{helpers → archived/helpers/archived}/modcall.py +0 -0
  88. /smftools/informatics/{helpers → archived/helpers/archived}/ohe_batching.py +0 -0
  89. /smftools/informatics/{helpers → archived/helpers/archived}/ohe_layers_decode.py +0 -0
  90. /smftools/informatics/{helpers → archived/helpers/archived}/one_hot_decode.py +0 -0
  91. /smftools/informatics/{helpers → archived/helpers/archived}/one_hot_encode.py +0 -0
  92. /smftools/informatics/{subsample_pod5.py → archived/subsample_pod5.py} +0 -0
  93. /smftools/informatics/{helpers/binarize_converted_base_identities.py → binarize_converted_base_identities.py} +0 -0
  94. /smftools/informatics/{helpers/complement_base_list.py → complement_base_list.py} +0 -0
  95. {smftools-0.2.1.dist-info → smftools-0.2.3.dist-info}/WHEEL +0 -0
  96. {smftools-0.2.1.dist-info → smftools-0.2.3.dist-info}/licenses/LICENSE +0 -0
smftools-0.2.1.dist-info/entry_points.txt DELETED
@@ -1,2 +0,0 @@
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- [console_scripts]
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- smftools = smftools.cli:cli