deepchopper 1.3.0__cp310-abi3-macosx_11_0_arm64.whl

deepchopper/utils/rich_utils.py

@@ -0,0 +1,100 @@
+from collections.abc import Sequence
+from pathlib import Path
+
+import rich
+import rich.syntax
+import rich.tree
+from hydra.core.hydra_config import HydraConfig
+from lightning_utilities.core.rank_zero import rank_zero_only
+from omegaconf import DictConfig, OmegaConf, open_dict
+from rich.prompt import Prompt
+
+from . import pylogger
+
+log = pylogger.RankedLogger(__name__, rank_zero_only=True)
+
+
+@rank_zero_only
+def print_config_tree(
+    cfg: DictConfig,
+    print_order: Sequence[str] = (
+        "data",
+        "model",
+        "callbacks",
+        "logger",
+        "trainer",
+        "paths",
+        "extras",
+    ),
+    *,
+    resolve: bool = False,
+    save_to_file: bool = False,
+) -> None:
+    """Prints the contents of a DictConfig as a tree structure using the Rich library.
+
+    :param cfg: A DictConfig composed by Hydra.
+    :param print_order: Determines in what order config components are printed. Default is ``("data", "model",
+    "callbacks", "logger", "trainer", "paths", "extras")``.
+    :param resolve: Whether to resolve reference fields of DictConfig. Default is ``False``.
+    :param save_to_file: Whether to export config to the hydra output folder. Default is ``False``.
+    """
+    style = "dim"
+    tree = rich.tree.Tree("CONFIG", style=style, guide_style=style)
+
+    queue = []
+
+    # add fields from `print_order` to queue
+    for field in print_order:
+        queue.append(field) if field in cfg else log.warning(
+            f"Field '{field}' not found in config. Skipping '{field}' config printing..."
+        )
+
+    # add all the other fields to queue (not specified in `print_order`)
+    for field in cfg:
+        if field not in queue:
+            queue.append(field)
+
+    # generate config tree from queue
+    for field in queue:
+        branch = tree.add(field, style=style, guide_style=style)
+
+        config_group = cfg[field]
+        if isinstance(config_group, DictConfig):
+            branch_content = OmegaConf.to_yaml(config_group, resolve=resolve)
+        else:
+            branch_content = str(config_group)
+
+        branch.add(rich.syntax.Syntax(branch_content, "yaml"))
+
+    # print config tree
+    rich.print(tree)
+
+    # save config tree to file
+    if save_to_file:
+        with Path(cfg.paths.output_dir, "config_tree.log").open("w") as file:
+            rich.print(tree, file=file)
+
+
+@rank_zero_only
+def enforce_tags(cfg: DictConfig, *, save_to_file: bool = False) -> None:
+    """Prompts user to input tags from command line if no tags are provided in config.
+
+    :param cfg: A DictConfig composed by Hydra.
+    :param save_to_file: Whether to export tags to the hydra output folder. Default is ``False``.
+    """
+    if not cfg.get("tags"):
+        if "id" in HydraConfig().cfg.hydra.job:
+            raise ValueError("Specify tags before launching a multirun!")
+
+        log.warning("No tags provided in config. Prompting user to input tags...")
+        tags = Prompt.ask("Enter a list of comma separated tags", default="dev")
+        tags = [t.strip() for t in tags.split(",") if t != ""]
+
+        with open_dict(cfg):
+            cfg.tags = tags
+
+        log.info(f"Tags: {cfg.tags}")
+
+    if save_to_file:
+        with Path(cfg.paths.output_dir, "tags.log").open("w") as file:
+            rich.print(cfg.tags, file=file)

deepchopper/utils/utils.py

@@ -0,0 +1,138 @@
+from __future__ import annotations
+
+import warnings
+from importlib.util import find_spec
+from typing import TYPE_CHECKING, Any
+
+import torch
+
+from . import pylogger, rich_utils
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from omegaconf import DictConfig
+
+log = pylogger.RankedLogger(__name__, rank_zero_only=True)
+
+
+def extras(cfg: DictConfig) -> None:
+    """Applies optional utilities before the task is started.
+
+    Utilities:
+        - Ignoring python warnings
+        - Setting tags from command line
+        - Rich config printing
+
+    :param cfg: A DictConfig object containing the config tree.
+    """
+    # return if no `extras` config
+    if not cfg.get("extras"):
+        log.warning("Extras config not found! <cfg.extras=null>")
+        return
+
+    # disable python warnings
+    if cfg.extras.get("ignore_warnings"):
+        log.info("Disabling python warnings! <cfg.extras.ignore_warnings=True>")
+        warnings.filterwarnings("ignore")
+
+    # prompt user to input tags from command line if none are provided in the config
+    if cfg.extras.get("enforce_tags"):
+        log.info("Enforcing tags! <cfg.extras.enforce_tags=True>")
+        rich_utils.enforce_tags(cfg, save_to_file=True)
+
+    # pretty print config tree using Rich library
+    if cfg.extras.get("print_config"):
+        log.info("Printing config tree with Rich! <cfg.extras.print_config=True>")
+        rich_utils.print_config_tree(cfg, resolve=True, save_to_file=True)
+
+
+def task_wrapper(task_func: Callable) -> Callable:
+    """Optional decorator that controls the failure behavior when executing the task function.
+
+    This wrapper can be used to:
+        - make sure loggers are closed even if the task function raises an exception (prevents multirun failure)
+        - save the exception to a `.log` file
+        - mark the run as failed with a dedicated file in the `logs/` folder (so we can find and rerun it later)
+        - etc. (adjust depending on your needs)
+
+    Example:
+    ```
+    @utils.task_wrapper
+    def train(cfg: DictConfig) -> Tuple[Dict[str, Any], Dict[str, Any]]:
+        ...
+        return metric_dict, object_dict
+    ```
+
+    :param task_func: The task function to be wrapped.
+
+    :return: The wrapped task function.
+    """
+
+    def wrap(cfg: DictConfig) -> tuple[dict[str, Any], dict[str, Any]]:
+        # execute the task
+        try:
+            metric_dict, object_dict = task_func(cfg=cfg)
+
+        # things to do if exception occurs
+        except Exception as ex:
+            # save exception to `.log` file
+            log.exception("")
+
+            # some hyperparameter combinations might be invalid or cause out-of-memory errors
+            # so when using hparam search plugins like Optuna, you might want to disable
+            # raising the below exception to avoid multirun failure
+            raise ex
+
+        # things to always do after either success or exception
+        finally:
+            # display output dir path in terminal
+            log.info(f"Output dir: {cfg.paths.output_dir}")
+
+            # always close wandb run (even if exception occurs so multirun won't fail)
+            if find_spec("wandb"):  # check if wandb is installed
+                import wandb
+
+                if wandb.run:
+                    log.info("Closing wandb!")
+                    wandb.finish()
+
+        return metric_dict, object_dict
+
+    return wrap
+
+
+def get_metric_value(metric_dict: dict[str, Any], metric_name: str | None) -> float | None:
+    """Safely retrieves value of the metric logged in LightningModule.
+
+    :param metric_dict: A dict containing metric values.
+    :param metric_name: If provided, the name of the metric to retrieve.
+    :return: If a metric name was provided, the value of the metric.
+    """
+    if not metric_name:
+        log.info("Metric name is None! Skipping metric value retrieval...")
+        return None
+
+    if metric_name not in metric_dict:
+        msg = (
+            f"Metric value not found! <metric_name={metric_name}>\n"
+            "Make sure metric name logged in LightningModule is correct!\n"
+            "Make sure `optimized_metric` name in `hparams_search` config is correct!"
+        )
+        raise Exception(msg)
+
+    metric_value = metric_dict[metric_name].item()
+    log.info(f"Retrieved metric value! <{metric_name}={metric_value}>")
+
+    return metric_value
+
+
+def device():
+    """Returns the appropriate device to use for training."""
+    if torch.cuda.is_available():
+        return torch.device("cuda")
+
+    if torch.backends.mps.is_available():
+        return torch.device("mps")
+
+    return torch.device("cpu")

deepchopper-1.3.0.dist-info/METADATA

@@ -0,0 +1,254 @@
+Metadata-Version: 2.4
+Name: deepchopper
+Version: 1.3.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering
+Requires-Dist: torch>=2.6.0
+Requires-Dist: lightning>=2.1.2
+Requires-Dist: torchmetrics>=1.2.1
+Requires-Dist: rich>=13.7.0
+Requires-Dist: transformers>=4.37.2
+Requires-Dist: safetensors>=0.4.2
+Requires-Dist: datasets>=3.0.0
+Requires-Dist: evaluate>=0.4.3
+Requires-Dist: typer>=0.12.0
+Requires-Dist: gradio==5.0.1
+Requires-Dist: fastapi==0.112.2
+Requires-Dist: scikit-learn>=1.5.2
+Requires-Dist: hydra-core>=1.3.2
+Requires-Dist: omegaconf>=2.3.0
+Requires-Dist: pyfastx>=2.2.0
+Requires-Dist: deepchopper-cli>=1.3.0
+License-File: LICENSE
+Summary: Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing
+Keywords: deep learning,bioinformatics,rust
+Home-Page: https://serde.rs
+Author-email: Yangyang Li <<yangyang.li@northwestern.edu>>, Ting-you Wang <<tywang@northwestern.edu>>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: changelog, https://github.com/ylab-hi/DeepChopper/README.md
+Project-URL: documentation, https://github.com/ylab-hi/DeepChopper
+Project-URL: homepage, https://github.com/ylab-hi/DeepChopper
+Project-URL: repository, https://github.com/ylab-hi/DeepChopper
+
+# <img src="./documentation/logo.webp" alt="logo" height="100"/> **DeepChopper** [![social](https://img.shields.io/github/stars/ylab-hi/DeepChopper?style=social)](https://github.com/ylab-hi/DeepChopper/stargazers)
+
+[![pypi](https://img.shields.io/pypi/v/deepchopper.svg)](https://pypi.python.org/pypi/deepchopper)
+[![PyPI - Wheel](https://img.shields.io/pypi/wheel/deepchopper)](https://pypi.org/project/deepchopper/#files)
+[![license](https://img.shields.io/pypi/l/deepchopper.svg)](https://github.com/ylab-hi/DeepChopper/blob/main/LICENSE)
+[![pypi version](https://img.shields.io/pypi/pyversions/deepchopper.svg)](https://pypi.python.org/pypi/deepbiop)
+[![platform](https://img.shields.io/badge/platform-linux%20%7C%20osx%20%7C%20win-blue)](https://pypi.org/project/deepchopper/#files)
+[![Actions status](https://github.com/ylab-hi/DeepChopper/actions/workflows/release-python.yml/badge.svg)](https://github.com/ylab-hi/DeepChopper/actions)
+[![Space](https://huggingface.co/datasets/huggingface/badges/resolve/main/open-in-hf-spaces-md.svg)](https://huggingface.co/spaces/yangliz5/deepchopper)
+
+<!--toc:start-->
+
+- [**DeepChopper**](#-deepchopper-)
+  - [🚀 Quick Start: Try DeepChopper Online](#-quick-start-try-deepchopper-online)
+  - [📦 Installation](#-installation)
+    - [Compatibility and Support](#compatibility-and-support)
+      - [PyPI Support](#pypi-support)
+  - [🛠️ Usage](#%EF%B8%8F-usage)
+    - [Command-Line Interface](#command-line-interface)
+    - [Python Library](#python-library)
+  - [📚 Cite](#-cite)
+  - [🤝 Contribution](#-contribution)
+    - [Build Environment](#build-environment)
+  - [📬 Support](#-support)
+
+<!--toc:end-->
+
+🧬 DeepChopper leverages a language model to accurately detect and chop artificial sequences that may cause chimeric reads, ensuring higher quality and more reliable sequencing results.
+By integrating seamlessly with existing workflows, DeepChopper provides a robust solution for researchers and bioinformaticians working with Nanopore direct-RNA sequencing data.
+
+📘 **FEATURED:** We provide a comprehensive tutorial that includes an example dataset in our [full documentation](./documentation/tutorial.md).
+
+## 🚀 Quick Start: Try DeepChopper Online
+
+Experience DeepChopper instantly through our user-friendly web interface. No installation required!
+Simply click the button below to launch the web application and start exploring DeepChopper's capabilities:
+
+[![Open in Hugging Face Spaces](https://huggingface.co/datasets/huggingface/badges/resolve/main/open-in-hf-spaces-md.svg)](https://huggingface.co/spaces/yangliz5/deepchopper)
+
+**What you can do online:**
+
+- 📤 Upload your sequencing data
+- 🔬 Run DeepChopper's analysis
+- 📊 Visualize results
+- 🎛️ Experiment with different parameters
+
+Perfect for quick tests or demonstrations! However, for extensive analyses or custom workflows, we recommend installing DeepChopper locally.
+
+> ⚠️ Note: The online version is limited to one FASTQ record at a time and may not be suitable for large-scale projects.
+
+## 📦 Installation
+
+DeepChopper can be installed using pip, the Python package installer.
+Follow these steps to install:
+
+1. Ensure you have Python 3.10 or later installed on your system.
+
+2. Create a virtual environment (recommended):
+
+   ```bash
+   python -m venv deepchopper_env
+   source deepchopper_env/bin/activate  # On Windows use `deepchopper_env\Scripts\activate`
+   ```
+
+3. Install DeepChopper:
+
+   ```bash
+   pip install deepchopper
+   ```
+
+4. Verify the installation:
+
+   ```bash
+   deepchopper --help
+   ```
+
+### Compatibility and Support
+
+DeepChopper is designed to work across various platforms and Python versions.
+Below are the compatibility matrices for PyPI installations:
+
+#### [PyPI Support][pypi]
+
+| Python Version | Linux x86_64 | macOS Intel | macOS Apple Silicon | Windows x86_64 |
+| :------------: | :----------: | :---------: | :-----------------: | :------------: |
+| 3.10 | ✅ | ✅ | ✅ | ✅ |
+| 3.11 | ✅ | ✅ | ✅ | ✅ |
+| 3.12 | ✅ | ✅ | ✅ | ✅ |
+
+🆘 Trouble installing? Check our [Troubleshooting Guide](https://github.com/ylab-hi/DeepChopper/blob/main/documentation/tutorial.md#troubleshooting) or [open an issue](https://github.com/ylab-hi/DeepChopper/issues).
+
+## 🛠️ Usage
+
+For a comprehensive guide, check out our [full tutorial](./documentation/tutorial.md).
+Here's a quick overview:
+
+### Command-Line Interface
+
+DeepChopper offers three main commands: `encode`, `predict`, and `chop`.
+
+1. **Encode** your input data:
+
+   ```bash
+   deepchopper encode <input.fq>
+   ```
+
+2. **Predict** chimera artifacts:
+
+   ```bash
+   deepchopper predict <input.parquet> --output predictions
+   ```
+
+   Using GPUs? Add the `--gpus` flag:
+
+   ```bash
+   deepchopper predict <input.parquet> --output predictions --gpus 2
+   ```
+
+3. **Chop** chimera artifacts:
+
+   ```bash
+   deepchopper chop <predictions> raw.fq
+   ```
+
+   **Memory Optimization:** For large datasets (>5M reads), use the `--chunk-size` parameter to control memory usage:
+
+   ```bash
+   # Low memory (~1-2GB): Slower but memory-efficient
+   deepchopper chop <predictions> raw.fq --chunk-size 1000
+
+   # Balanced (default, ~5-10GB): Good balance of speed and memory
+   deepchopper chop <predictions> raw.fq --chunk-size 10000
+
+   # High performance (~20-50GB): Fastest, requires more memory
+   deepchopper chop <predictions> raw.fq --chunk-size 50000
+   ```
+
+   The chop command uses **streaming mode** to minimize memory usage. Instead of loading all reads into memory at once (which can require 100GB+ for 20M reads), it processes records in configurable chunks and writes results incrementally.
+
+Want a GUI? Launch the web interface (note: limited to one FASTQ record at a time):
+
+```bash
+deepchopper web
+```
+
+### Python Library
+
+Integrate DeepChopper into your Python scripts:
+
+```python
+import deepchopper
+
+model = deepchopper.DeepChopper.from_pretrained("yangliz5/deepchopper")
+# Your analysis code here
+```
+
+## 📚 Cite
+
+If DeepChopper aids your research, please cite [our paper](https://www.nature.com/articles/s41467-026-68571-5):
+
+```bibtex
+@article{li2026genomic,
+  title = {Genomic Language Model Mitigates Chimera Artifacts in Nanopore Direct {{RNA}} Sequencing},
+  author = {Li, Yangyang and Wang, Ting-You and Guo, Qingxiang and Ren, Yanan and Lu, Xiaotong and Cao, Qi and Yang, Rendong},
+  date = {2026-01-19},
+  journaltitle = {Nature Communications},
+  shortjournal = {Nat Commun},
+  publisher = {Nature Publishing Group},
+  issn = {2041-1723},
+  doi = {10.1038/s41467-026-68571-5},
+  url = {https://www.nature.com/articles/s41467-026-68571-5},
+  urldate = {2026-01-20}
+}
+```
+
+## 🤝 Contribution
+
+We welcome contributions! Here's how to set up your development environment:
+
+### Build Environment
+
+Install [UV](https://docs.astral.sh/uv/getting-started/installation/#installation-methods) and [Rust](https://www.rust-lang.org/tools/install)
+
+```bash
+git clone https://github.com/ylab-hi/DeepChopper.git
+cd DeepChopper
+
+# Install dependencies
+uv sync
+
+# Run DeepChopper
+uv run deepchopper --help
+```
+
+🎉 Ready to contribute? Check out our [Contribution Guidelines](./CONTRIBUTING.md) to get started!
+
+## 📬 Support
+
+Need help? Have questions?
+
+- 📖 Check our [Documentation](./documentation/tutorial.md)
+- 🐛 [Report issues](https://github.com/ylab-hi/DeepChopper/issues)
+
+______________________________________________________________________
+
+DeepChopper is developed with ❤️ by the YLab team.
+Happy sequencing! 🧬🔬
+
+[pypi]: https://pypi.python.org/pypi/deepchopper
+

deepchopper-1.3.0.dist-info/RECORD

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+deepchopper/utils/print.py,sha256=6WibNTPeZzBWmM6vfE_BqYKjWsZZIU9liG1yNsaKzlg,3072
+deepchopper/utils/pylogger.py,sha256=_09Z3fnoSI2udjkwR_sCMO8fVImYh1HMS-k4KrCxrKI,2512
+deepchopper/utils/rich_utils.py,sha256=FFgIxnetoe5b9YNSN9ASaqRSZiztB7zJDWd6EBW3x2o,3283
+deepchopper/utils/utils.py,sha256=reIctC8RP3fQeGpD8tw9ifgOh4MWPi8t0nxWN17fT6s,4623
+deepchopper-1.3.0.dist-info/METADATA,sha256=IOpSt1JY7JCZALRhw7fy_pbfatutXh5uOTglfhXa0Lc,9420
+deepchopper-1.3.0.dist-info/WHEEL,sha256=vZ12AMAE5CVtd8oYbYGrz3omfHuIZCNO_3P50V00s00,104
+deepchopper-1.3.0.dist-info/entry_points.txt,sha256=sX2f2aZ_wguUzA9yw3Lr17DBBjjV9DBdcIuKeKk3r78,50
+deepchopper-1.3.0.dist-info/licenses/LICENSE,sha256=Yo7RMo69x4zRi_3gBAdmi55FFQWk3MVJghEU3H2eDkE,11354
+deepchopper-1.3.0.dist-info/RECORD,,

deepchopper-1.3.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: maturin (1.11.5)
+Root-Is-Purelib: false
+Tag: cp310-abi3-macosx_11_0_arm64

deepchopper-1.3.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+deepchopper=deepchopper.cli:app