Metadata-Version: 2.1
Name: pydamage
Version: 0.60
Summary: Damage parameter estimation for ancient DNA
Home-page: https://github.com/maxibor/pydamage
License: GNU-GPLv3
Description: <p align="center">
            <a href="https://github.com/maxibor/pydamage"><img src="https://github.com/maxibor/pydamage/raw/master/docs/img/logo.png" alt="PyDamage"></a>
        </p>
        
        <p align="center">
            <a href="https://github.com/maxibor/pydamage/releases"><img src="https://img.shields.io/github/v/release/maxibor/pydamage?include_prereleases&label=version"/></a>
            <a href="https://github.com/maxibor/pydamage/actions"><img src="https://github.com/maxibor/pydamage/workflows/pydamage_ci/badge.svg"/></a>
            <a href="https://readthedocs.org/projects/pydamage/badge/?version=latest"><img src="https://readthedocs.org/projects/pydamage/badge/?version=latest"/></a>
            <a href="https://pypi.org/project/pydamage/"><img src="https://img.shields.io/pypi/v/pydamage"/></a>
            <a href="https://anaconda.org/maxibor/pydamage"><img src="https://img.shields.io/conda/v/maxibor/pydamage"/></a>
        </p>
        
        # PyDamage
        
        Pydamage, is a Python software to automate the process of contig damage identification and estimation.
        After modelling the ancient DNA damage using the C to T transitions, Pydamage uses a likelihood ratio test to discriminate between truly ancient, and modern contigs originating from sample contamination.
        
        ## Installation
        
        ### With [conda](https://docs.conda.io/en/latest/) (recommended)
        
        ```bash
        conda install -c conda-forge -c bioconda -c maxibor pydamage
        ```
        
        ### With pip
        
        ```bash
        pip install pydamage
        ```
        
        ### Install from source to use the development version
        
        Using pip
        
        ```bash
        pip install git+ssh://git@github.com/maxibor/pydamage.git@dev
        ```
        
        By cloning in a dedicated conda environment
        
        ```bash
        git clone git@github.com:maxibor/pydamage.git
        cd pydamage
        git checkout dev
        conda env create -f environment.yml
        conda activate pydamage
        pip install -e .
        ```
        
        
        ## Quick start
        
        ```bash
        pydamage --outdir result_directory analyze aligned.bam
        ```
        
        > Note that if you specify `--outdir`, it has to be before the PyDamage subcommand, example: `pydamage --outdir test filter pydamage_results.csv`
        
        ## CLI help
        
        Command line interface help message
        
        ```bash
        pydamage --help
        ```
        
        ## Documentation
        
        [pydamage.readthedocs.io](https://pydamage.readthedocs.io)
        
        ## Cite
        
        ```
        @article{Borry2021_pydamage,
            author = {Borry, Maxime and Huebner, Alexander and Rohrlach, Adam B and Warinner, Christina G},
            doi = {10.1101/2021.03.24.436838},
            elocation-id = {2021.03.24.436838},
            eprint = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838.full.pdf},
            journal = {bioRxiv},
            publisher = {Cold Spring Harbor Laboratory},
            title = {PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly},
            url = {https://www.biorxiv.org/content/early/2021/03/24/2021.03.24.436838},
            year = {2021}
        }
        ```
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
