Metadata-Version: 2.1
Name: pydamage
Version: 0.2
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)
        
        [![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) [![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, 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.
        
        ## Install
        
        ### 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
        ```
        
        
        ## Documentation
        
        [pydamage.readthedocs.io](https://pydamage.readthedocs.io)
        
        ## Help
        
        ```bash
        $ pydamage --help
        Usage: pydamage [OPTIONS] BAM
        
          PyDamage: Damage parameter estimation for ancient DNA
          Author: Maxime Borry
          Contact: <borry[at]shh.mpg.de>
          Homepage & Documentation: github.com/maxibor/pydamage
        
          BAM: path to BAM/SAM/CRAM alignment file
        
        Options:
          --version              Show the version and exit.
          -w, --wlen INTEGER     Window length for damage modeling  [default: 35]
          -p, --process INTEGER  Number of processes  [default: 2]
          -m, --mini INTEGER     Minimum reads aligned to consider reference
                                 [default: 1000]
        
          -c, --cov FLOAT        Minimum coverage to consider reference  [default:8]
        
          -s, --show_al          Show alignments representations
          -pl, --plot            Make the damage plots
          --verbose              Verbose mode
          -o, --outdir PATH      Output directory  [default: pydamage_results]
          --force                Force overwriting of results directory
          --help                 Show this message and exit.
        ```
        
        > **pydamage logic: `n_reads >=minimum reads OR coverage >= minimum coverage`**
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
