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.
- smftools/_version.py +1 -1
- smftools/cli/helpers.py +32 -6
- smftools/cli/hmm_adata.py +232 -31
- smftools/cli/latent_adata.py +318 -0
- smftools/cli/load_adata.py +77 -73
- smftools/cli/preprocess_adata.py +178 -53
- smftools/cli/spatial_adata.py +149 -101
- smftools/cli_entry.py +12 -0
- smftools/config/conversion.yaml +11 -1
- smftools/config/default.yaml +38 -1
- smftools/config/experiment_config.py +53 -1
- smftools/constants.py +65 -0
- smftools/hmm/HMM.py +88 -0
- smftools/informatics/__init__.py +6 -0
- smftools/informatics/bam_functions.py +358 -8
- smftools/informatics/converted_BAM_to_adata.py +584 -163
- smftools/informatics/h5ad_functions.py +115 -2
- smftools/informatics/modkit_extract_to_adata.py +1003 -425
- smftools/informatics/sequence_encoding.py +72 -0
- smftools/logging_utils.py +21 -2
- smftools/metadata.py +1 -1
- smftools/plotting/__init__.py +9 -0
- smftools/plotting/general_plotting.py +2411 -628
- smftools/plotting/hmm_plotting.py +85 -7
- smftools/preprocessing/__init__.py +1 -0
- smftools/preprocessing/append_base_context.py +17 -17
- smftools/preprocessing/append_mismatch_frequency_sites.py +158 -0
- smftools/preprocessing/calculate_consensus.py +1 -1
- smftools/preprocessing/calculate_read_modification_stats.py +6 -1
- smftools/readwrite.py +53 -17
- smftools/schema/anndata_schema_v1.yaml +15 -1
- smftools/tools/__init__.py +4 -0
- smftools/tools/calculate_leiden.py +57 -0
- smftools/tools/calculate_nmf.py +119 -0
- smftools/tools/calculate_umap.py +91 -8
- smftools/tools/rolling_nn_distance.py +235 -0
- smftools/tools/tensor_factorization.py +169 -0
- {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/METADATA +8 -6
- {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/RECORD +42 -35
- {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/WHEEL +0 -0
- {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/entry_points.txt +0 -0
- {smftools-0.3.0.dist-info → smftools-0.3.1.dist-info}/licenses/LICENSE +0 -0
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Metadata-Version: 2.3
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Name: smftools
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Version: 0.3.
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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/
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Requires-Dist: captum; 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'
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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: igraph; extra == 'cluster'
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Requires-Dist: leidenalg; extra == 'cluster'
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Provides-Extra: dev
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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: 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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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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[](https://pypi.org/project/smftools)
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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=
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smftools/cli_entry.py,sha256=
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smftools/metadata.py,sha256
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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=
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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=
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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=
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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/direct.yaml,sha256=Jw8Nj3QKQrCfJpVl8sGgCKdRvjk5cV66dzRlNfoDOzI,2269
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smftools/config/discover_input_files.py,sha256=NcOqNYoXggLDieam8UMJAc2sWmoYOZ_Wqp2mApnlBfs,4015
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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=
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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/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/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=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=wGsvk51FhrByNPI-TCgZEh0nKyW6jd1t_mHR6957IAo,17577
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smftools/informatics/pod5_functions.py,sha256=6_EA2StpslOe0phSwR9TDB_U-Tmx4ykuBcTAiOL0LPU,10327
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