Metadata-Version: 2.3
Name: smftools
Version: 0.3.0
Summary: Single Molecule Footprinting Analysis in Python.
Project-URL: Source, https://github.com/jkmckenna/smftools
Project-URL: Documentation, https://smftools.readthedocs.io/
Author: Joseph McKenna
Maintainer-email: Joseph McKenna <jkmckenna@berkeley.edu>
License: MIT License
        
        Copyright (c) 2024 jkmckenna
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Keywords: anndata,chromatin-accessibility,machine-learning,nanopore,protein-dna-binding,single-locus,single-molecule-footprinting
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.10
Requires-Dist: anndata>=0.10.0
Requires-Dist: biopython>=1.79
Requires-Dist: click
Requires-Dist: numpy<2,>=1.22.0
Requires-Dist: pandas>=1.4.2
Requires-Dist: scipy>=1.7.3
Requires-Dist: tqdm
Provides-Extra: all
Requires-Dist: captum; extra == 'all'
Requires-Dist: fastcluster; extra == 'all'
Requires-Dist: hydra-core; extra == 'all'
Requires-Dist: igraph; extra == 'all'
Requires-Dist: leidenalg; extra == 'all'
Requires-Dist: lightning; extra == 'all'
Requires-Dist: matplotlib>=3.6.2; extra == 'all'
Requires-Dist: multiqc; extra == 'all'
Requires-Dist: networkx>=3.2; extra == 'all'
Requires-Dist: omegaconf; extra == 'all'
Requires-Dist: pod5>=0.1.21; extra == 'all'
Requires-Dist: pybedtools>=0.12.0; extra == 'all'
Requires-Dist: pybigwig>=0.3.24; extra == 'all'
Requires-Dist: pysam>=0.19.1; extra == 'all'
Requires-Dist: scanpy>=1.9; extra == 'all'
Requires-Dist: scikit-learn>=1.0.2; extra == 'all'
Requires-Dist: seaborn>=0.11; extra == 'all'
Requires-Dist: shap; extra == 'all'
Requires-Dist: torch>=1.9.0; extra == 'all'
Requires-Dist: upsetplot; extra == 'all'
Requires-Dist: wandb; extra == 'all'
Provides-Extra: cluster
Requires-Dist: fastcluster; extra == 'cluster'
Requires-Dist: leidenalg; extra == 'cluster'
Provides-Extra: dev
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Provides-Extra: docs
Requires-Dist: ipython>=7.20; extra == 'docs'
Requires-Dist: matplotlib!=3.6.1; extra == 'docs'
Requires-Dist: myst-nb<2,>=1; extra == 'docs'
Requires-Dist: myst-parser<3,>=2; extra == 'docs'
Requires-Dist: nbsphinx>=0.9; extra == 'docs'
Requires-Dist: pyyaml; extra == 'docs'
Requires-Dist: readthedocs-sphinx-search; extra == 'docs'
Requires-Dist: setuptools; extra == 'docs'
Requires-Dist: sphinx-autodoc-typehints<4,>=1.25.2; extra == 'docs'
Requires-Dist: sphinx-book-theme<2,>=1.1; extra == 'docs'
Requires-Dist: sphinx-click<7,>=5; extra == 'docs'
Requires-Dist: sphinx-copybutton<0.6,>=0.5; extra == 'docs'
Requires-Dist: sphinx-design; extra == 'docs'
Requires-Dist: sphinx<8,>=7; extra == 'docs'
Requires-Dist: sphinxcontrib-bibtex<3,>=2; extra == 'docs'
Requires-Dist: sphinxext-opengraph<0.10,>=0.9; extra == 'docs'
Provides-Extra: misc
Requires-Dist: networkx>=3.2; extra == 'misc'
Requires-Dist: upsetplot; extra == 'misc'
Provides-Extra: ml-base
Requires-Dist: scikit-learn>=1.0.2; extra == 'ml-base'
Requires-Dist: torch>=1.9.0; extra == 'ml-base'
Provides-Extra: ml-extended
Requires-Dist: captum; extra == 'ml-extended'
Requires-Dist: hydra-core; extra == 'ml-extended'
Requires-Dist: lightning; extra == 'ml-extended'
Requires-Dist: omegaconf; extra == 'ml-extended'
Requires-Dist: shap; extra == 'ml-extended'
Requires-Dist: wandb; extra == 'ml-extended'
Provides-Extra: ont
Requires-Dist: pod5>=0.1.21; extra == 'ont'
Provides-Extra: plotting
Requires-Dist: matplotlib>=3.6.2; extra == 'plotting'
Requires-Dist: seaborn>=0.11; extra == 'plotting'
Provides-Extra: pybedtools
Requires-Dist: pybedtools>=0.12.0; extra == 'pybedtools'
Provides-Extra: pybigwig
Requires-Dist: pybigwig>=0.3.24; extra == 'pybigwig'
Provides-Extra: pysam
Requires-Dist: pysam>=0.19.1; extra == 'pysam'
Provides-Extra: qc
Requires-Dist: multiqc; extra == 'qc'
Provides-Extra: scanpy
Requires-Dist: igraph; extra == 'scanpy'
Requires-Dist: scanpy>=1.9; extra == 'scanpy'
Provides-Extra: torch
Requires-Dist: torch>=1.9.0; extra == 'torch'
Description-Content-Type: text/markdown

[![PyPI](https://img.shields.io/pypi/v/smftools.svg)](https://pypi.org/project/smftools)
[![Docs](https://readthedocs.org/projects/smftools/badge/?version=latest)](https://smftools.readthedocs.io/en/latest/?badge=latest)

# smftools
A Python tool for processing raw sequencing data derived from single molecule footprinting experiments into [anndata](https://anndata.readthedocs.io/en/latest/) objects. Additional functionality for preprocessing, spatial analyses, and HMM based feature annotation.

## Philosophy
While genomic data structures (SAM/BAM) were built to handle low-coverage data (<1000X) along large references, smftools prioritizes high-coverage data (scalable to >1,000,000X coverage) of a few genomic loci at a time. This enables efficient data storage, rapid data operations, hierarchical metadata handling, seamless integration with various machine-learning packages, and ease of visualization. Furthermore, functionality is modularized, enabling analysis sessions to be saved, reloaded, and easily shared with collaborators. Analyses are centered around the [anndata](https://anndata.readthedocs.io/en/latest/) object, and are heavily inspired by the work conducted within the single-cell genomics community.

## Dependencies
The following CLI tools need to be installed and configured before using the informatics (smftools.inform) module of smftools, which is used by the smftools load CLI command:
1) [Dorado](https://github.com/nanoporetech/dorado) -> Basecalling, alignment, demultiplexing. Required for Nanopore SMF experiments, but not Illumina SMF experiments.
2) [Minimap2](https://github.com/lh3/minimap2) -> Aligner if not using dorado. Support for other aligners could eventually be added if needed.
3) [Modkit](https://github.com/nanoporetech/modkit) -> Extracting read level methylation metrics from the MM/ML tags in BAM files. Only required for direct modification detection SMF protocols.
