smftools 0.3.0__py3-none-any.whl → 0.3.1__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 (42) hide show
  1. smftools/_version.py +1 -1
  2. smftools/cli/helpers.py +32 -6
  3. smftools/cli/hmm_adata.py +232 -31
  4. smftools/cli/latent_adata.py +318 -0
  5. smftools/cli/load_adata.py +77 -73
  6. smftools/cli/preprocess_adata.py +178 -53
  7. smftools/cli/spatial_adata.py +149 -101
  8. smftools/cli_entry.py +12 -0
  9. smftools/config/conversion.yaml +11 -1
  10. smftools/config/default.yaml +38 -1
  11. smftools/config/experiment_config.py +53 -1
  12. smftools/constants.py +65 -0
  13. smftools/hmm/HMM.py +88 -0
  14. smftools/informatics/__init__.py +6 -0
  15. smftools/informatics/bam_functions.py +358 -8
  16. smftools/informatics/converted_BAM_to_adata.py +584 -163
  17. smftools/informatics/h5ad_functions.py +115 -2
  18. smftools/informatics/modkit_extract_to_adata.py +1003 -425
  19. smftools/informatics/sequence_encoding.py +72 -0
  20. smftools/logging_utils.py +21 -2
  21. smftools/metadata.py +1 -1
  22. smftools/plotting/__init__.py +9 -0
  23. smftools/plotting/general_plotting.py +2411 -628
  24. smftools/plotting/hmm_plotting.py +85 -7
  25. smftools/preprocessing/__init__.py +1 -0
  26. smftools/preprocessing/append_base_context.py +17 -17
  27. smftools/preprocessing/append_mismatch_frequency_sites.py +158 -0
  28. smftools/preprocessing/calculate_consensus.py +1 -1
  29. smftools/preprocessing/calculate_read_modification_stats.py +6 -1
  30. smftools/readwrite.py +53 -17
  31. smftools/schema/anndata_schema_v1.yaml +15 -1
  32. smftools/tools/__init__.py +4 -0
  33. smftools/tools/calculate_leiden.py +57 -0
  34. smftools/tools/calculate_nmf.py +119 -0
  35. smftools/tools/calculate_umap.py +91 -8
  36. smftools/tools/rolling_nn_distance.py +235 -0
  37. smftools/tools/tensor_factorization.py +169 -0
  38. {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/METADATA +8 -6
  39. {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/RECORD +42 -35
  40. {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/WHEEL +0 -0
  41. {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/entry_points.txt +0 -0
  42. {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/licenses/LICENSE +0 -0
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: smftools
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- Version: 0.3.0
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+ Version: 0.3.1
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  Summary: Single Molecule Footprinting Analysis in Python.
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  Project-URL: Source, https://github.com/jkmckenna/smftools
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  Project-URL: Documentation, https://smftools.readthedocs.io/
@@ -55,7 +55,6 @@ Provides-Extra: all
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  Requires-Dist: captum; extra == 'all'
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  Requires-Dist: fastcluster; extra == 'all'
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  Requires-Dist: hydra-core; extra == 'all'
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- Requires-Dist: igraph; extra == 'all'
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  Requires-Dist: leidenalg; extra == 'all'
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  Requires-Dist: lightning; extra == 'all'
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  Requires-Dist: matplotlib>=3.6.2; extra == 'all'
@@ -65,16 +64,18 @@ Requires-Dist: omegaconf; extra == 'all'
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  Requires-Dist: pod5>=0.1.21; extra == 'all'
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  Requires-Dist: pybedtools>=0.12.0; extra == 'all'
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  Requires-Dist: pybigwig>=0.3.24; extra == 'all'
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+ Requires-Dist: pynndescent>=0.5.10; extra == 'all'
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  Requires-Dist: pysam>=0.19.1; extra == 'all'
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- Requires-Dist: scanpy>=1.9; extra == 'all'
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  Requires-Dist: scikit-learn>=1.0.2; extra == 'all'
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  Requires-Dist: seaborn>=0.11; extra == 'all'
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  Requires-Dist: shap; extra == 'all'
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  Requires-Dist: torch>=1.9.0; extra == 'all'
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+ Requires-Dist: umap-learn>=0.5.5; extra == 'all'
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  Requires-Dist: upsetplot; extra == 'all'
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  Requires-Dist: wandb; extra == 'all'
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  Provides-Extra: cluster
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  Requires-Dist: fastcluster; extra == 'cluster'
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+ Requires-Dist: igraph; extra == 'cluster'
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  Requires-Dist: leidenalg; extra == 'cluster'
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  Provides-Extra: dev
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  Requires-Dist: pre-commit; extra == 'dev'
@@ -103,6 +104,7 @@ Requires-Dist: networkx>=3.2; extra == 'misc'
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  Requires-Dist: upsetplot; extra == 'misc'
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  Provides-Extra: ml-base
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  Requires-Dist: scikit-learn>=1.0.2; extra == 'ml-base'
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+ Requires-Dist: tensorly; extra == 'ml-base'
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  Requires-Dist: torch>=1.9.0; extra == 'ml-base'
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  Provides-Extra: ml-extended
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  Requires-Dist: captum; extra == 'ml-extended'
@@ -124,11 +126,11 @@ Provides-Extra: pysam
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  Requires-Dist: pysam>=0.19.1; extra == 'pysam'
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  Provides-Extra: qc
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  Requires-Dist: multiqc; extra == 'qc'
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- Provides-Extra: scanpy
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- Requires-Dist: igraph; extra == 'scanpy'
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- Requires-Dist: scanpy>=1.9; extra == 'scanpy'
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  Provides-Extra: torch
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  Requires-Dist: torch>=1.9.0; extra == 'torch'
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+ Provides-Extra: umap
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+ Requires-Dist: pynndescent>=0.5.10; extra == 'umap'
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+ Requires-Dist: umap-learn>=0.5.5; extra == 'umap'
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  Description-Content-Type: text/markdown
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  [![PyPI](https://img.shields.io/pypi/v/smftools.svg)](https://pypi.org/project/smftools)
@@ -1,32 +1,33 @@
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  smftools/__init__.py,sha256=Wun5eO3FHy7sAelTLlLdFj3NurqZFQxfO3U5YHJ3KcY,1247
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  smftools/_settings.py,sha256=QqZzjz6Y_-gZH4VJAPRCL68HRlGjzl3hXU7d-dMi8-M,418
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- smftools/_version.py,sha256=KdHlm9KKc9XEB182bG2710ZrIpNwJdS5TBcAjXA8U_M,58
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- smftools/cli_entry.py,sha256=wTjwx520HJIez2I1CGXAHhWXUC-nsRBZ6yUFJd_84XM,10519
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- smftools/constants.py,sha256=SWOJ76KTP2p3geyVkNQ8LB96NOmDDtjFEur2hSw7iyU,1289
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- smftools/logging_utils.py,sha256=jOptBgSW7NQcw7JTnw2-oWcN2qyrtfJkDpIZsfcU1Mk,1323
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- smftools/metadata.py,sha256=yGTMof2hAUR43QfgRSwK9mnOiTAznV3Usxzsvt185s4,14898
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+ smftools/_version.py,sha256=e9cd8nKFi-8fyxRlTRJYWgSHyt1C_r_TE3kQS7NeJv0,58
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+ smftools/cli_entry.py,sha256=Mfhg8GWqER0AHYqKB2McocljX3OWcaYFOEfDrR3WGbQ,10808
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+ smftools/constants.py,sha256=atMoOE3wM803ixhE_PdklOYbNhJvh-37gNkOyg9Jtnw,4007
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+ smftools/logging_utils.py,sha256=OpDul2P5FCWhjJqunYK2MrSaYtbKEPGFE0Z7vZhSX0Y,2193
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+ smftools/metadata.py,sha256=-U8jVzjBsXbZ2SKRcyPHMCDPnsQQRR4djzerjpeQvzU,14917
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  smftools/optional_imports.py,sha256=PpjWa-H-rlxwXJjkPLSHkiuim922xwDVsqlgFY8wWqw,1039
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- smftools/readwrite.py,sha256=GCCBAWXQezTtXMBr-2NeV-jJfdnl_yB_x5nuz7Bt11c,52413
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+ smftools/readwrite.py,sha256=ZOy54ABP4fcSe37-bGyhhd8kKOaVXPMCB-WFn_rrOwg,53665
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  smftools/cli/__init__.py,sha256=U4S_2y3zgLZVfMenHRaJFBW8yqh2mUBuI291LGQVOJ8,35
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- smftools/cli/helpers.py,sha256=Euf0e3rNgKAlnghlJvr5fKaiMxqPum1HD6CYI__Z3Ko,1435
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- smftools/cli/hmm_adata.py,sha256=2W1OLU_KaEtwUzkL_ZaecK4rQA9XyHJEurZEKQqnU00,40795
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- smftools/cli/load_adata.py,sha256=mVsXQQB8sRIIettJhC1Y1xnrBcSTrRs-p-O72TlhO1o,32453
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- smftools/cli/preprocess_adata.py,sha256=m_IWvUEBwIA5goJ2W7FQdqaA8tqQZB7gAXjjCWrcFCU,22632
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- smftools/cli/spatial_adata.py,sha256=rzEPJ5pM78zE27rp-Sgif0fw_I6NiPK71xyGnZnXYcc,32001
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+ smftools/cli/helpers.py,sha256=Oj5wrdjrZHNqyPrmwaaPoQ_QvuM-b7e_A4osyrYsf-A,2432
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+ smftools/cli/hmm_adata.py,sha256=068V4qBCodW6xCZEkTWOkz0QHZ3UuixhTKAipFLimxE,48284
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+ smftools/cli/latent_adata.py,sha256=O9CPbm0ru4pFOENQmvTDzUINKLiSYeTOR671vJnyxJU,10431
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+ smftools/cli/load_adata.py,sha256=7-wsYIRs-axh2U4LYm0JtgpCNpWQntxkU-9X4nuz9Fc,31606
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+ smftools/cli/preprocess_adata.py,sha256=A7P5JvBhlUtl2Pepu5yHigzgRDmhDp7uwJS8DWyBZEk,28294
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+ smftools/cli/spatial_adata.py,sha256=xRoYYGtGI4msiZVy68fISLjMlbWDhKQYFe6l1n0zKtM,34273
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  smftools/cli/archived/cli_flows.py,sha256=w1rPHSH8WzZn7owz0ra7WOUGlJSEsaRw_W3x-9Ra42k,4977
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  smftools/config/__init__.py,sha256=rcI3qG1DGfRcvQzh8bffiHuRPcmPsas5T8MN6uhScxA,106
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- smftools/config/conversion.yaml,sha256=N7lUO7-yAaJR6VhxRGCRc-ceAi0cp5xNASSIsXl9KwI,1242
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+ smftools/config/conversion.yaml,sha256=ih5qu1gMSOFmjHU1JLqgQ9CzekWD5vKQQREWnIm0HX0,1498
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  smftools/config/deaminase.yaml,sha256=JCE1nF39AX436-3RyvuZN24gdJfriDijNv5XNHrMT8I,1357
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- smftools/config/default.yaml,sha256=yhcMASjqqccuHpTFepyjt6KHfNNR6IDNSH0rmEERXm4,13933
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+ smftools/config/default.yaml,sha256=yyATffMZbyLuiTQ6dpq4pNFvAgYp1CTntAdGA30R4wM,14976
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  smftools/config/direct.yaml,sha256=Jw8Nj3QKQrCfJpVl8sGgCKdRvjk5cV66dzRlNfoDOzI,2269
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  smftools/config/discover_input_files.py,sha256=NcOqNYoXggLDieam8UMJAc2sWmoYOZ_Wqp2mApnlBfs,4015
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- smftools/config/experiment_config.py,sha256=IqSN7JwnnWWjOoDZWbQ2zATwjm_uywSSs8mhagII6ms,67521
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+ smftools/config/experiment_config.py,sha256=7KoibibpZxz_rRuOj8QiU9gvuMhwMtlF2sbw6EZeszE,70415
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  smftools/datasets/F1_hybrid_NKG2A_enhander_promoter_GpC_conversion_SMF.h5ad.gz,sha256=q6wJtgFRDln0o20XNCx1qad3lwcdCoylqPN7wskTfI8,2926497
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  smftools/datasets/F1_sample_sheet.csv,sha256=9PodIIOXK2eamYPbC6DGnXdzgi9bRDovf296j1aM0ak,259
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  smftools/datasets/__init__.py,sha256=_G08ZAMlA9zpY5UjWTVlpAbW2YPS4PLCmz5g1pZdcCw,157
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  smftools/datasets/dCas9_m6A_invitro_kinetics.h5ad.gz,sha256=niOcVHaYY7h3XyvwSkN-V_NMBaRt2vTP5TrJO0CwMCs,8385050
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  smftools/datasets/datasets.py,sha256=-VOdONP-K_ftLDtLktRKbq3S6vSB4pzRQ6VYBxAy_4A,1074
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- smftools/hmm/HMM.py,sha256=_kYhqfmz46XBbx9Y12KF6dKp2XPcSHreZiQgavgx6h4,82437
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+ smftools/hmm/HMM.py,sha256=Yq7awVwCtTPb4HET1UIx2VTHVvgiwu_2pjEgZTTkTP4,85660
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  smftools/hmm/__init__.py,sha256=vs-fjo-v9y8EwdoErK6KDBm-YzD_XmTtflsdTJlRgTg,746
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  smftools/hmm/call_hmm_peaks.py,sha256=CzTEz3EP_LNLirIVYzRxbV7_5fCBpLa9azLPSEt6s7s,13529
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  smftools/hmm/display_hmm.py,sha256=N94hmEKZGehPdsB9yLyY7U1_tTWDk2NTMU-PuWnEQqA,1321
@@ -36,20 +37,21 @@ smftools/hmm/archived/apply_hmm_batched.py,sha256=W2-qx1XbcDJz4q38YCxb1eQn9h-hqA
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  smftools/hmm/archived/calculate_distances.py,sha256=MfBhXZNkjQvu9Y8LVMDpiQ4aS9uyfa4TUQbLGjQ1aM0,680
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  smftools/hmm/archived/call_hmm_peaks.py,sha256=6SklWXCn4H8LnlGvBncIsLhnf2gaNy8Qro_jxGJn7I0,5249
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  smftools/hmm/archived/train_hmm.py,sha256=sYF4RTEKPhE6MwK2eTAv4ghf-f7_33-FvhwUG6tegTU,2513
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- smftools/informatics/__init__.py,sha256=jxyzu37yR1lho4LP3WhQ6_Oez4f-un7vCqP80s8xR3g,2885
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- smftools/informatics/bam_functions.py,sha256=ErTV3ZrguIaGAqMnLnf-0QmfvvDRix0h_ehSRqKU2Ls,59008
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+ smftools/informatics/__init__.py,sha256=Q2l7iGOEuZXtGmqWG3NwF-_vNwl4VmJPsElg7-eANO0,3226
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+ smftools/informatics/bam_functions.py,sha256=b_Vb08HmOl8-hXLbkVNBw-zl-1loXqw-yQJkklJUvyY,73636
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  smftools/informatics/basecalling.py,sha256=PgjWoOgfQaUOCoKpyaKO8m8sauMW3el6wdEtzGlvy4s,3699
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  smftools/informatics/bed_functions.py,sha256=9y3XNNl6QivqkWEfoH5XszP3Qsj0P-rCopgfd0HpFgs,21268
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  smftools/informatics/binarize_converted_base_identities.py,sha256=KRL-KT8MYADadHgRbTgoOFD30LlZazKHe10Hz9nO6Z4,7850
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  smftools/informatics/complement_base_list.py,sha256=6DInlD4cdjKJmmUv4Cp4UU9HHLe60Pm8RF9AoBfBfF0,571
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- smftools/informatics/converted_BAM_to_adata.py,sha256=YU7KBHgr0ulYZBv0I9PKI-p71JMZRvJbY9SlECWcQ3Q,25741
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+ smftools/informatics/converted_BAM_to_adata.py,sha256=CIIrJVQHFpc2gg7K1W99kpmG5IUVBVqQIRBPKuR4EHk,42759
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  smftools/informatics/fasta_functions.py,sha256=MD-fL0BkExiDXMUSPkHaHrkOK7aqzOozWREGr5Gzw8w,14111
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- smftools/informatics/h5ad_functions.py,sha256=fX4CgO9ZSgYh9VbCmgGPXwNg5uolLJoNPcBZgzNwgMk,13167
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- smftools/informatics/modkit_extract_to_adata.py,sha256=wcat5i002BxBpSMPCLENDdu-cnH0K87p6NN1vFSbfc4,63551
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+ smftools/informatics/h5ad_functions.py,sha256=wGsvk51FhrByNPI-TCgZEh0nKyW6jd1t_mHR6957IAo,17577
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+ smftools/informatics/modkit_extract_to_adata.py,sha256=oL1dxcNLCsGqFngZd3HYW63tBzkGKQx9kbCWOAzwwfc,84454
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  smftools/informatics/modkit_functions.py,sha256=BvWd_qulVOQKZJFMd4pLTVD3ruo1dT48BmvQsdHB0_E,6103
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  smftools/informatics/ohe.py,sha256=fdMEdXG45hiCsHtmYkPsXJKLJ-SBaZktdGx-bmfI3a0,5997
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  smftools/informatics/pod5_functions.py,sha256=6_EA2StpslOe0phSwR9TDB_U-Tmx4ykuBcTAiOL0LPU,10327
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  smftools/informatics/run_multiqc.py,sha256=M67HhO5FIJl8qn3Qc9YUlnbk7kdDWyYVL0B9SenrqMo,1115
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+ smftools/informatics/sequence_encoding.py,sha256=9u6E1IcUFL6Cn2BOWW4l_VYY9qQ-6KJo7M1bprMLV30,2244
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@@ -121,27 +123,28 @@ smftools/machine_learning/training/train_sklearn_model.py,sha256=zQ5SQpu_sl7IVcZ
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  smftools/machine_learning/utils/grl.py,sha256=ptr-08dRKAGBZ1cySy_B90GgMn5kXtNXlcUC4PJ5mNA,485
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- smftools/plotting/__init__.py,sha256=JrfnlocBQdW2QeP207PDUcx_4DMiOPLszxZBBml9POw,1478
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+ smftools/plotting/__init__.py,sha256=GA-fyueJMOgQYe3EH6juWZ3wNYo0ugUqKyoBlubWOoc,2100
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  smftools/plotting/classifiers.py,sha256=9Qt0eixvgE3WXl6jcwPm7O3ATA7Q6mfqRh_B_9M2qTQ,16749
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- smftools/plotting/general_plotting.py,sha256=ShN8R0yauo-Br_IDy3ZlM5VR3wuetFaEtLxK5r6Nn8A,69455
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- smftools/plotting/hmm_plotting.py,sha256=wPROxP-IJj-lY1I70s5YYy-H-XFfbcVol8PS2aw7srQ,11644
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+ smftools/plotting/general_plotting.py,sha256=TZeIJOCLuNzeUDktee2HP9LJO-o1clNPcPaZ64WHFLk,134703
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+ smftools/plotting/hmm_plotting.py,sha256=3UkhfbZYM0hXvSoQJ94F2GR70cTPjpfm9w2nOo8itL0,14964
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  smftools/plotting/qc_plotting.py,sha256=ODK8UrjVrAJeG8Qfu09DmAJ_o9GJaXRxGwN0pEgbHAU,10358
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- smftools/preprocessing/__init__.py,sha256=l_oNlEOjrzoAZbTa66y9prIkEPbGcH4F1J2MyyMmesE,1855
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- smftools/preprocessing/append_base_context.py,sha256=Z18Izb9-gZ4_ifXOHFZqcmPOradjCiyJZMZ5oTDfiLQ,7102
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+ smftools/preprocessing/__init__.py,sha256=x-QTdVOYbVPpHqO2cBPhmsO-6AliemcBb2Qo78cQrqw,1952
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+ smftools/preprocessing/append_base_context.py,sha256=sZfgkhYzXYtsNO-XgMcQ4v2Hl1u6agaHCpmx-s3jCVY,7134
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+ smftools/preprocessing/append_mismatch_frequency_sites.py,sha256=ZOE6rXAM0D4ElvTi-XJ6iriJielx7Afb4ewgHTyiWBA,6048
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- smftools/preprocessing/calculate_read_modification_stats.py,sha256=L1X0LatpjPI5wA1j7MjFgukePYGo75DcgJCYPlhVAGM,5319
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- smftools/tools/__init__.py,sha256=MqvwhrFQsTvoSpbJ4HIzV9LWwNLef0RXe9iI3VZReMI,976
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- smftools/tools/calculate_umap.py,sha256=oj4EJP4M3cZ50T0bYNVAfZAssEG9ZxKmNgjgKmqxf-g,3594
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+ smftools/schema/anndata_schema_v1.yaml,sha256=FCMjYIqgt-YxQxehcgkdwWBzqk1k-aSZ3fUcksX1bH4,8310
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+ smftools/tools/__init__.py,sha256=M1FF2r0z-thHmU397w_VB2TiEJfmGQyLiYzf264xlB8,1242
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+ smftools/tools/calculate_leiden.py,sha256=48Y72NIzGb6yxtnUund7gS_2jIFro5lwJC0ycNOoAJI,1867
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+ smftools/tools/calculate_nmf.py,sha256=O5IC9G5CrWdhefHaOPOkyx0Jiro_DZ4mvF75psEP4Q8,4192
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+ smftools/tools/calculate_umap.py,sha256=N5cPHMosPPFkp9NInYVZiTGcbJtFsQhFccHDKQG7yhI,6258
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+ smftools/tools/rolling_nn_distance.py,sha256=mhoTWBwD1-HmktpQ5yOAz5Q8u2BMkp8RegTMKj5FFC4,8255
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- smftools-0.3.0.dist-info/METADATA,sha256=JuAG9ifECVbhIjC2lKmIqgzosM1Ao2naUcmGh7zgpHk,7840
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- smftools-0.3.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
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- smftools-0.3.0.dist-info/entry_points.txt,sha256=q4hg4w-mKkI2leekM_-YZc5XRJzp96Mh1FcU3hac82g,52
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- smftools-0.3.0.dist-info/licenses/LICENSE,sha256=F8LwmL6vMPddaCt1z1S83Kh_OZv50alTlY7BvVx1RXw,1066
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- smftools-0.3.0.dist-info/RECORD,,
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+ smftools-0.3.1.dist-info/METADATA,sha256=BN-jDQTEhEUhQ4JHTxlHIgWqHNyfxLKNFWupYqOOPVg,7958
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+ smftools-0.3.1.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
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+ smftools-0.3.1.dist-info/entry_points.txt,sha256=q4hg4w-mKkI2leekM_-YZc5XRJzp96Mh1FcU3hac82g,52
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+ smftools-0.3.1.dist-info/licenses/LICENSE,sha256=F8LwmL6vMPddaCt1z1S83Kh_OZv50alTlY7BvVx1RXw,1066
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+ smftools-0.3.1.dist-info/RECORD,,