pyaging 0.0.1__tar.gz → 0.0.4__tar.gz

{pyaging-0.0.1 → pyaging-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyaging
-Version: 0.0.1
+Version: 0.0.4
 Summary: A Python-based compendium of GPU-optimized aging clocks.
 License: BSD
 Author: Lucas Paulo de Lima Camillo
@@ -13,12 +13,12 @@ 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: anndata (>=0.10.3,<0.11.0)
+Requires-Dist: numpy (>=1.26.2,<2.0.0)
+Requires-Dist: pandas (>=2.1.3,<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)
+Requires-Dist: scikit-learn (>=1.3.2,<2.0.0)
+Requires-Dist: torch (>=2.1.1,<3.0.0)
 Project-URL: homepage, https://github.com/rsinghlab/pyaging
 Project-URL: repository, https://github.com/rsinghlab/pyaging
 Description-Content-Type: text/markdown
@@ -43,29 +43,18 @@ Description-Content-Type: text/markdown
 
 `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)
+[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) - [Blood chemistry](https://pyaging.readthedocs.io/en/latest/tutorial_bloodchemistry.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!
+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! We are also happy to adapt to any licensing terms for commercial entities.
 
 ## 💬 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-0.0.4}/README.md

@@ -18,29 +18,18 @@
 
 `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)
+[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) - [Blood chemistry](https://pyaging.readthedocs.io/en/latest/tutorial_bloodchemistry.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!
+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! We are also happy to adapt to any licensing terms for commercial entities.
 
 ## 💬 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-0.0.4}/pyaging/data/_data.py

@@ -4,6 +4,7 @@ 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
 
@@ -21,7 +22,9 @@ def download_example_data(
     Parameters
     ----------
     data_type : str
-        The type of data to download. Valid options are 'methylation', 'histone_mark', 'rnaseq', and 'atac'.
+        The type of data to download. Valid options are 'GSE139307' (human methylation),
+        'GSE223748' (mammalian methylation), 'ENCFF386QWG' (histone mark),
+        'GSE65765' (C. elegans RNA-seq), 'atac_example' (ATAC-Seq), 'blood_chemistry_example' (blood chemistry).
 
     dir : str
         The directory to deposit the downloaded file. Defaults to "pyaging_data".
@@ -61,6 +64,7 @@ def download_example_data(
         "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",
+        "blood_chemistry_example": "https://pyaging.s3.amazonaws.com/example_data/blood_chemistry_example.pkl",
     }
 
     if data_type not in list(data_type_to_url.keys()):

{pyaging-0.0.1 → pyaging-0.0.4}/pyaging/logger/_logger.py

@@ -273,7 +273,8 @@ class Logger:
         self.logger_stream_handler.terminator = saved_terminator
 
     def start_progress(self, message, indent_level=1, *args, **kwargs):
-        self.log_time()
+        now = time.time()
+        self.previous_timestamp = now
         message = format_logging_message(
             "⚙️ " + message, logging.INFO, indent_level=indent_level
         )
@@ -281,8 +282,8 @@ class Logger:
         self.logger_stream_handler.flush()
 
     def finish_progress(self, progress_name="", time_unit="s", indent_level=1):
-        # self.log_time()
-        # self.report_progress(percent=100, progress_name=progress_name)#
+        now = time.time()
+        self.time_passed = now - self.previous_timestamp
 
         saved_terminator = self.logger_stream_handler.terminator
         self.logger_stream_handler.terminator = ""

{pyaging-0.0.1 → pyaging-0.0.4}/pyaging/predict/__init__.py

@@ -1,5 +1,6 @@
 # pyaging/predict/__init__.py
 
 from ._pred import *
+from ._pred_utils import *
 from ._preprocessing import *
 from ._postprocessing import *

{pyaging-0.0.1 → pyaging-0.0.4}/pyaging/predict/_postprocessing.py

@@ -35,3 +35,15 @@ def anti_log_log(x):
     """
     # Double transformation: logarithmic followed by anti-logarithmic
     return math.exp(-math.exp(-x))
+
+
+def mortality_to_phenoage(x):
+    """
+    Applies a convertion from a CDF of the mortality score from a Gompertz
+    distribution to phenotypic age.
+    """
+    # lambda
+    l = 0.0192
+    mortality_score = 1 - math.exp(-math.exp(x) * (math.exp(120 * l) - 1) / l)
+    age = 141.50225 + math.log(-0.00553 * math.log(1 - mortality_score)) / 0.090165
+    return age

pyaging-0.0.4/pyaging/predict/_pred.py

@@ -0,0 +1,137 @@
+import anndata
+
+from ._pred_utils import *
+
+
+def predict_age(
+    adata: anndata.AnnData,
+    clock_names: str = "horvath2013",
+    dir: str = "pyaging_data",
+    verbose: bool = True,
+) -> anndata.AnnData:
+    """
+    Predicts biological age using specified aging clocks.
+
+    This function takes an AnnData object and applies one or more specified aging
+    clock models to predict the biological age of the samples. It handles the entire pipeline from data
+    preprocessing, model loading, prediction, to postprocessing. It also enriches the input AnnData
+    object with the predicted ages and relevant clock metadata.
+
+    Parameters
+    ----------
+    adata: AnnData
+        An AnnData object. The object should have .X attribute for the
+        data matrix and .var_names for feature names.
+
+    clock_names: str or list of str, optional
+        Names of the aging clocks to be applied. It can be a single clock name as a string or a list
+        of clock names, by default "horvath2013".
+
+    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.
+
+    Returns
+    -------
+    AnnData
+        The input AnnData object enriched with the predicted ages and clock metadata in the .obs and
+        .uns attributes, respectively.
+
+    Notes
+    -----
+    The function is designed to be flexible and can handle both single and multiple clock predictions.
+    The predicted ages are appended to the .obs attribute of the AnnData object with the clock name as
+    the key. The metadata of each clock used in the prediction is stored in the .uns attribute.
+
+    It is important that the input AnnData object's .X attribute contains data suitable for age 
+    prediction.
+
+    The function automatically handles the transfer of data and models to the appropriate compute
+    device (CPU or GPU) based on system configuration.
+
+    Examples
+    --------
+    >>> adata = anndata.read_h5ad("sample_data.h5ad")
+    >>> adata = predict_age(adata, clock_names=["horvath2013", "hannum"])
+    >>> adata.obs["horvath2013"]  # Access predicted ages by clock name
+
+    """
+    logger = LoggerManager.gen_logger("predict_age")
+    if not verbose:
+        silence_logger("predict_age")
+    logger.first_info("Starting predict_age function")
+
+    # Ensure clock_names is a list
+    if isinstance(clock_names, str):
+        clock_names = [clock_names]
+
+    # Set device for PyTorch operations
+    device = set_torch_device(logger)
+
+    for clock_name in clock_names:
+        logger.info(f"🕒 Processing clock: {clock_name}", indent_level=1)
+
+        # Load and prepare the clock
+        clock_name = clock_name.lower()
+        features, weight_dict, preprocessing, postprocessing, preprocessing_helper, postprocessing_helper = load_clock(
+            clock_name, dir, logger, indent_level=2
+        )
+
+        # Check and update adata for missing features
+        adata = check_features_in_adata(
+            adata, clock_name, features, logger, indent_level=2
+        )
+
+        # Apply preprocessing 
+        if preprocessing:
+            adata = preprocess_data(
+                adata, preprocessing, preprocessing_helper, features, logger, indent_level=2
+            )
+            
+        # Filter features and then extract data matrix
+        x_numpy = filter_features_and_extract_data(
+            adata, preprocessing, features, logger, indent_level=2
+        )
+
+        # Convert numpy array to tensor
+        x_tensor = convert_numpy_array_to_tensor(
+            x_numpy, device, logger, indent_level=2
+        )
+
+        # Initialize and configure the model
+        clock_model = initialize_model(
+            clock_name, features, weight_dict, device, logger, indent_level=2
+        )
+
+        # Perform age prediction using the model
+        predicted_ages_tensor = predict_ages_with_model(
+            clock_model, x_tensor, logger, indent_level=2
+        )
+
+        # Convert adata tensor to numpy array
+        predicted_ages = convert_tensor_to_numpy_array(
+            predicted_ages_tensor, logger, indent_level=2
+        )
+
+        # Apply postprocessing if specified
+        if postprocessing:
+            predicted_ages = postprocess_data(
+                predicted_ages, postprocessing, postprocessing_helper, logger, indent_level=2
+            )
+
+        # Add predicted ages to adata
+        add_pred_ages_adata(adata, predicted_ages, clock_name, logger, indent_level=2)
+
+        # Load all clocks metadata
+        all_clock_metadata = load_clock_metadata(dir, logger, indent_level=2)
+        
+        # Add clock metadata to adata object
+        add_clock_metadata_adata(
+            adata, clock_name, all_clock_metadata, logger, indent_level=2
+        )
+        
+
+    logger.done()
+    return adata