pyaging 0.0.1__tar.gz

pyaging-0.0.1/LICENSE

@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2023, Lucas Paulo de Lima Camillo
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

pyaging-0.0.1/PKG-INFO

@@ -0,0 +1,72 @@
+Metadata-Version: 2.1
+Name: pyaging
+Version: 0.0.1
+Summary: A Python-based compendium of GPU-optimized aging clocks.
+License: BSD
+Author: Lucas Paulo de Lima Camillo
+Author-email: lucas_camillo@alumni.brown.edu
+Requires-Python: >=3.9,<4.0
+Classifier: License :: Other/Proprietary License
+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
+Provides-Extra: docs
+Requires-Dist: anndata (>=0.10.0,<0.11.0)
+Requires-Dist: numpy (>=1.26.0,<2.0.0)
+Requires-Dist: pandas (>=2.0.0,<3.0.0)
+Requires-Dist: pyBigWig (>=0.3.22,<0.4.0)
+Requires-Dist: scikit-learn (>=1.3.0,<2.0.0)
+Requires-Dist: torch (>=2.0.0,<3.0.0)
+Project-URL: homepage, https://github.com/rsinghlab/pyaging
+Project-URL: repository, https://github.com/rsinghlab/pyaging
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <img height="160" src="docs/_static/logo.png" />
+</p>
+
+##
+
+[![test](https://github.com/rsinghlab/pyaging/actions/workflows/test.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/test.yml)
+[![build](https://github.com/rsinghlab/pyaging/actions/workflows/build.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/build.yml)
+[![publish](https://github.com/rsinghlab/pyaging/actions/workflows/publish.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/publish.yml)
+[![release](https://github.com/rsinghlab/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/release.yml)
+[![documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
+[![beta](https://img.shields.io/badge/status-beta-yellow)](https://github.com/rsinghlab/pyaging)
+[![upload](https://img.shields.io/pypi/v/pyaging?logo=PyPI)](https://pypi.org/project/pyaging/) 
+[![download](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
+[![star](https://img.shields.io/github/stars/rsinghlab/pyaging?logo=GitHub&color=red)](https://github.com/rsinghlab/pyaging/stargazers)
+
+## 🐍 **pyaging**: a Python-based compendium of GPU-optimized aging clocks
+
+`pyaging` is a cutting-edge Python package designed for the longevity research community, offering a comprehensive suite of GPU-optimized biological aging clocks.
+
+[Installation](https://pyaging.readthedocs.io/en/latest/installation.html) - [Search, cite, and get metadata](https://pyaging.readthedocs.io/en/latest/tutorial_utils.html) - [Bulk DNA methylation](https://pyaging.readthedocs.io/en/latest/tutorial_dnam.html) - [Bulk histone mark ChIP-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_histonemarkchipseq.html) - [Bulk ATAC-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_atacseq.html) - [Bulk RNA-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_rnaseq.html) - [API Reference](https://pyaging.readthedocs.io/en/latest/pyaging.html)
+
+With a growing number of aging clocks, comparing and analyzing them can be challenging. `pyaging` simplifies this process, allowing researchers to input various molecular layers (DNA methylation, histone ChIP-Seq, ATAC-seq, transcriptomics, etc.) and quickly analyze them using multiple aging clocks, thanks to its GPU-backed infrastructure. This makes it an ideal tool for large datasets and multi-layered analysis.
+
+## 📝 To-Do List
+
+- [X] Integrate `black` for PEP8 compliant code formatting
+- [X] Improve and expand `readthedocs` documentation
+- [X] Add option to specify download directory for datasets
+- [X] Rename datasets to reflect source publications
+- [X] Include mammalian array example datasets
+- [X] Add feature to control logging verbosity
+- [ ] Publish to PyPi
+- [ ] Add percentage of missing features in anndata after age prediction for each clock
+- [ ] Add table in readthedocs with all clock metadata
+- [ ] Add and populate "Notes" tab in metadata
+- [ ] Integrate scAge and scRNAseq clocks (and datasets)
+- [ ] Incorporate murine DNA methylation and proteomic clocks (and datasets)
+- [ ] Add PhenoAge based on blood chemistry analysis (and datasets)
+
+## ❓ Can't find an aging clock?
+
+If you have recently developed an aging clock and would like it to be integrated into `pyaging`, please [email us](lucas_camillo@alumni.brown.edu). We aim to incorporate it within two weeks!
+
+## 💬 Community Discussion
+For coding-related queries, feedback, and discussions, please visit our [GitHub Issues](https://github.com/rsinghlab/pyaging/issues) page.
+

pyaging-0.0.1/README.md

@@ -0,0 +1,46 @@
+<p align="center">
+  <img height="160" src="docs/_static/logo.png" />
+</p>
+
+##
+
+[![test](https://github.com/rsinghlab/pyaging/actions/workflows/test.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/test.yml)
+[![build](https://github.com/rsinghlab/pyaging/actions/workflows/build.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/build.yml)
+[![publish](https://github.com/rsinghlab/pyaging/actions/workflows/publish.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/publish.yml)
+[![release](https://github.com/rsinghlab/pyaging/actions/workflows/release.yml/badge.svg)](https://github.com/rsinghlab/pyaging/actions/workflows/release.yml)
+[![documentation](https://readthedocs.org/projects/pyaging/badge/?version=latest)](https://pyaging.readthedocs.io/en/latest/)
+[![beta](https://img.shields.io/badge/status-beta-yellow)](https://github.com/rsinghlab/pyaging)
+[![upload](https://img.shields.io/pypi/v/pyaging?logo=PyPI)](https://pypi.org/project/pyaging/) 
+[![download](https://static.pepy.tech/badge/pyaging)](https://pepy.tech/project/pyaging)
+[![star](https://img.shields.io/github/stars/rsinghlab/pyaging?logo=GitHub&color=red)](https://github.com/rsinghlab/pyaging/stargazers)
+
+## 🐍 **pyaging**: a Python-based compendium of GPU-optimized aging clocks
+
+`pyaging` is a cutting-edge Python package designed for the longevity research community, offering a comprehensive suite of GPU-optimized biological aging clocks.
+
+[Installation](https://pyaging.readthedocs.io/en/latest/installation.html) - [Search, cite, and get metadata](https://pyaging.readthedocs.io/en/latest/tutorial_utils.html) - [Bulk DNA methylation](https://pyaging.readthedocs.io/en/latest/tutorial_dnam.html) - [Bulk histone mark ChIP-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_histonemarkchipseq.html) - [Bulk ATAC-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_atacseq.html) - [Bulk RNA-Seq](https://pyaging.readthedocs.io/en/latest/tutorial_rnaseq.html) - [API Reference](https://pyaging.readthedocs.io/en/latest/pyaging.html)
+
+With a growing number of aging clocks, comparing and analyzing them can be challenging. `pyaging` simplifies this process, allowing researchers to input various molecular layers (DNA methylation, histone ChIP-Seq, ATAC-seq, transcriptomics, etc.) and quickly analyze them using multiple aging clocks, thanks to its GPU-backed infrastructure. This makes it an ideal tool for large datasets and multi-layered analysis.
+
+## 📝 To-Do List
+
+- [X] Integrate `black` for PEP8 compliant code formatting
+- [X] Improve and expand `readthedocs` documentation
+- [X] Add option to specify download directory for datasets
+- [X] Rename datasets to reflect source publications
+- [X] Include mammalian array example datasets
+- [X] Add feature to control logging verbosity
+- [ ] Publish to PyPi
+- [ ] Add percentage of missing features in anndata after age prediction for each clock
+- [ ] Add table in readthedocs with all clock metadata
+- [ ] Add and populate "Notes" tab in metadata
+- [ ] Integrate scAge and scRNAseq clocks (and datasets)
+- [ ] Incorporate murine DNA methylation and proteomic clocks (and datasets)
+- [ ] Add PhenoAge based on blood chemistry analysis (and datasets)
+
+## ❓ Can't find an aging clock?
+
+If you have recently developed an aging clock and would like it to be integrated into `pyaging`, please [email us](lucas_camillo@alumni.brown.edu). We aim to incorporate it within two weeks!
+
+## 💬 Community Discussion
+For coding-related queries, feedback, and discussions, please visit our [GitHub Issues](https://github.com/rsinghlab/pyaging/issues) page.

pyaging-0.0.1/pyaging/__init__.py

@@ -0,0 +1,10 @@
+# pyaging/__init__.py
+
+from . import logger
+from . import data
+from . import utils
+from . import models
+from . import preprocess as pp
+from . import predict as pred
+
+__version__ = "0.1.0"

pyaging-0.0.1/pyaging/data/__init__.py

@@ -0,0 +1,3 @@
+# pyaging/data/__init__.py
+
+from ._data import *

pyaging-0.0.1/pyaging/data/_data.py

@@ -0,0 +1,75 @@
+import os
+import torch
+import ntpath
+import os
+from urllib.request import urlretrieve
+from functools import wraps
+from ..utils import progress, download
+from ..logger import LoggerManager, main_tqdm, silence_logger
+
+
+def download_example_data(
+    data_type: str, dir: str = "pyaging_data", verbose: bool = True
+) -> None:
+    """
+    Downloads example datasets for various types of biological data used in aging studies.
+
+    This function facilitates the download of example datasets for different types of biological data,
+    including methylation, histone mark, RNA-seq, and ATAC-seq data. It is designed to provide quick
+    access to standard datasets for users to test and explore the functionalities of the pyaging package.
+
+    Parameters
+    ----------
+    data_type : str
+        The type of data to download. Valid options are 'methylation', 'histone_mark', 'rnaseq', and 'atac'.
+
+    dir : str
+        The directory to deposit the downloaded file. Defaults to "pyaging_data".
+
+    verbose: bool
+        Whether to log the output to console with the logger. Defaults to True.
+
+    Raises
+    ------
+    ValueError
+        If the specified data_type is not implemented, a ValueError is raised with a message suggesting
+        the user to request its implementation.
+
+    Notes
+    -----
+    The function maps the specified data_type to its corresponding URL and then calls the `download`
+    function to retrieve the dataset. The datasets are sourced from AWS S3
+    and are chosen to represent typical data formats and structures used in aging research.
+
+    The downloaded data can be used for various analyses, including testing the pyaging package's
+    functionalities, learning data processing techniques, or as a benchmark for custom analyses.
+
+    Examples
+    --------
+    >>> download_example_data("methylation")
+    # This will download the example methylation dataset to the local system.
+
+    """
+    logger = LoggerManager.gen_logger("download_example_data")
+    if not verbose:
+        silence_logger("download_example_data")
+    logger.first_info("Starting download_example_data function")
+
+    data_type_to_url = {
+        "GSE139307": "https://pyaging.s3.amazonaws.com/example_data/GSE139307.pkl",
+        "GSE223748": "https://pyaging.s3.amazonaws.com/example_data/GSE223748_subset.pkl",
+        "ENCFF386QWG": "https://pyaging.s3.amazonaws.com/example_data/ENCFF386QWG.bigWig",
+        "GSE65765": "https://pyaging.s3.amazonaws.com/example_data/GSE65765_CPM.pkl",
+        "atac_example": "https://pyaging.s3.amazonaws.com/example_data/atac_example.pkl",
+    }
+
+    if data_type not in list(data_type_to_url.keys()):
+        logger.error(
+            f"Example data {data_type} has not yet been implemented in pyaging.",
+            indent_level=2,
+        )
+
+    url = data_type_to_url[data_type]
+    download(url, dir, logger, indent_level=1)
+
+    logger.done()

pyaging-0.0.1/pyaging/logger/__init__.py

@@ -0,0 +1,3 @@
+# pyaging/logger/__init__.py
+
+from ._logger import *