Metadata-Version: 2.1
Name: pydamage
Version: 0.40
Summary: Damage parameter estimation for ancient DNA
Home-page: https://github.com/maxibor/pydamage
License: GNU-GPLv3
Description: [![pydamage logo](https://github.com/maxibor/pydamage/raw/master/docs/img/logo.png)](https://github.com/maxibor/pydamage)
        [![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/maxibor/pydamage?include_prereleases&label=version)](https://github.com/maxibor/pydamage/releases) [![pydamage CI](https://github.com/maxibor/pydamage/workflows/pydamage_ci/badge.svg)](https://github.com/maxibor/pydamage/actions) [![Documentation Status](https://readthedocs.org/projects/pydamage/badge/?version=latest)](https://pydamage.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/pydamage)](https://pypi.org/project/pydamage/) [![Conda](https://img.shields.io/conda/v/maxibor/pydamage)](https://anaconda.org/maxibor/pydamage)
        
        # 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 aligned.bam reference.fa
        ```
        
        ## CLI help
        
        Command line interface help message
        
        ```bash
        pydamage --help
        ```
        
        ## Documentation
        
        [pydamage.readthedocs.io](https://pydamage.readthedocs.io)
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
