smftools 0.2.4__py3-none-any.whl → 0.3.0__py3-none-any.whl

smftools/tools/subset_adata.py

@@ -1,28 +1,30 @@
 # subset_adata
 
-def subset_adata(adata, columns, cat_type='obs'):
-    """
-    Adds subset metadata to an AnnData object based on categorical values in specified .obs or .var columns.
-    
-    Parameters:
-        adata (AnnData): The AnnData object to add subset metadata to.
-        columns (list of str): List of .obs or .var column names to subset by. The order matters.
-        cat_type (str): obs or var. Default is obs
-
-    Returns:
-        None
-    """
-    import pandas as pd
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Sequence
+
+if TYPE_CHECKING:
     import anndata as ad
 
-    subgroup_name = '_'.join(columns)
-    if 'obs' in cat_type:
+
+def subset_adata(adata: "ad.AnnData", columns: Sequence[str], cat_type: str = "obs") -> None:
+    """Add subset metadata based on categorical values in ``.obs`` or ``.var`` columns.
+
+    Args:
+        adata: AnnData object to annotate.
+        columns: Obs or var column names to subset by (order matters).
+        cat_type: ``"obs"`` or ``"var"``.
+    """
+
+    subgroup_name = "_".join(columns)
+    if "obs" in cat_type:
         df = adata.obs[columns]
-        adata.obs[subgroup_name] = df.apply(lambda row: '_'.join(row.astype(str)), axis=1)
-        adata.obs[subgroup_name] = adata.obs[subgroup_name].astype('category')
-    elif 'var' in cat_type:    
+        adata.obs[subgroup_name] = df.apply(lambda row: "_".join(row.astype(str)), axis=1)
+        adata.obs[subgroup_name] = adata.obs[subgroup_name].astype("category")
+    elif "var" in cat_type:
         df = adata.var[columns]
-        adata.var[subgroup_name] = df.apply(lambda row: '_'.join(row.astype(str)), axis=1)
-        adata.var[subgroup_name] = adata.var[subgroup_name].astype('category')
+        adata.var[subgroup_name] = df.apply(lambda row: "_".join(row.astype(str)), axis=1)
+        adata.var[subgroup_name] = adata.var[subgroup_name].astype("category")
 
-    return None
+    return None

smftools-0.3.0.dist-info/METADATA

@@ -0,0 +1,147 @@
+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'
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+Requires-Dist: scanpy>=1.9; extra == 'all'
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+Requires-Dist: seaborn>=0.11; extra == 'all'
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+Requires-Dist: torch>=1.9.0; extra == 'all'
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+Provides-Extra: cluster
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+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'
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+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.

smftools-0.3.0.dist-info/RECORD

@@ -0,0 +1,182 @@
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smftools-0.2.4.dist-info/METADATA

@@ -1,141 +0,0 @@
-Metadata-Version: 2.3
-Name: smftools
-Version: 0.2.4
-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 :: 2 - Pre-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 :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: <3.13,>=3.9
-Requires-Dist: anndata>=0.10.0
-Requires-Dist: biopython>=1.79
-Requires-Dist: captum
-Requires-Dist: click
-Requires-Dist: fastcluster
-Requires-Dist: hydra-core
-Requires-Dist: igraph
-Requires-Dist: leidenalg
-Requires-Dist: lightning
-Requires-Dist: multiqc
-Requires-Dist: networkx>=3.2
-Requires-Dist: numpy<2,>=1.22.0
-Requires-Dist: omegaconf
-Requires-Dist: pandas>=1.4.2
-Requires-Dist: pod5>=0.1.21
-Requires-Dist: pybedtools>=0.12.0
-Requires-Dist: pybigwig>=0.3.24
-Requires-Dist: pyfaidx>=0.8.0
-Requires-Dist: pysam>=0.19.1
-Requires-Dist: scanpy>=1.9
-Requires-Dist: scikit-learn>=1.0.2
-Requires-Dist: scipy>=1.7.3
-Requires-Dist: seaborn>=0.11
-Requires-Dist: shap
-Requires-Dist: torch>=1.9.0
-Requires-Dist: tqdm
-Requires-Dist: upsetplot
-Requires-Dist: wandb
-Provides-Extra: docs
-Requires-Dist: ipython>=7.20; extra == 'docs'
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-Requires-Dist: sphinx>=7; extra == 'docs'
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-Provides-Extra: tests
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-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:
-1) [Dorado](https://github.com/nanoporetech/dorado) -> Basecalling, alignment, demultiplexing.
-2) [Minimap2](https://github.com/lh3/minimap2) -> Alignment if not using dorado.
-3) [Modkit](https://github.com/nanoporetech/modkit) -> Extracting read level methylation metrics from modified BAM files. Only required for direct modification detection (ie methylation).
-
-## Main Commands
-### smftools load: Processes raw Nanopore/Illumina data from SMF experiments into an AnnData object.
-![](docs/source/_static/smftools_informatics_diagram.png)
-### smftools preprocess: Appends QC metrics to the AnnData object and performs filtering.
-![](docs/source/_static/smftools_preprocessing_diagram.png)
-### smftools spatial: Appends spatial analyses to the AnnData object.
-- Currently Includes: Position X Position correlation matrices, clustering, dimensionality reduction, spatial autocorrelation. 
-### smftools hmm: Fits a basic HMM to each sample and appends HMM feature layers
-- Main outputs wills be stored in adata.layers
-### smftools batch <command>: Performs batch processing on a csv of config file pathes for any of the above commands.
-- Nice when analyzing multiple experiments
-### smftools concatenate: Concatenates a list or directory of anndata objects.
-- Mainly used for combining multiple experiments into a single anndata object.
-
-## Announcements
-
-### 12/02/25 - Version 0.2.3 is available through PyPI
-Version 0.2.3 provides the core smftools functionality through several command line commands (load, preprocess, spatial, hmm).
-
-### 11/05/25 - Version 0.2.1 is available through PyPI
-Version 0.2.1 makes the core workflow (smftools load) a command line tool that takes in an experiment_config.csv file for input/output and parameter management.
-
-### 05/29/25 - Version 0.1.6 is available through PyPI.
-Informatics, preprocessing, tools, plotting modules have core functionality that is approaching stability on MacOS(Intel/Silicon) and Linux(Ubuntu). I will work on improving documentation/tutorials shortly. The base PyTorch/Scikit-Learn ML-infrastructure is going through some organizational changes to work with PyTorch Lightning, Hydra, and WanDB to facilitate organizational scaling, multi-device usage, and logging.
-
-### 10/01/24 - More recent versions are being updated frequently. Installation from source over PyPI is recommended!
-
-### 09/09/24 - The version 0.1.1 package ([smftools-0.1.1](https://pypi.org/project/smftools/)) is installable through pypi!
-The informatics module has been bumped to alpha-phase status. This module can deal with POD5s and unaligned BAMS from nanopore conversion and direct SMF experiments, as well as FASTQs from Illumina conversion SMF experiments. Primary output from this module is an AnnData object containing all relevant SMF data, which is compatible with all downstream smftools modules. The other modules are still in pre-alpha phase. Preprocessing, Tools, and Plotting modules should be promoted to alpha-phase within the next month or so.
-
-### 08/30/24 - The version 0.1.0 package ([smftools-0.1.0](https://pypi.org/project/smftools/)) is installable through pypi!
-Currently, this package (smftools-0.1.0) is going through rapid improvement (dependency handling accross Linux and Mac OS, testing, documentation, debugging) and is still too early in development for widespread use. The underlying functionality was originally developed as a collection of scripts for single molecule footprinting (SMF) experiments in our lab, but is being packaged/developed to facilitate the expansion of SMF to any lab that is interested in performing these styles of experiments/analyses. The alpha-phase package is expected to be available within a couple months, so stay tuned!