pydamage 0.1

Damage parameter estimation for ancient DNA

Pydamage, is a Python software to automate the process of contig damage identification and estimation. It uses a process akin to a likelihood ratio test to attempt to discriminate between truly ancient, and modern contigs originating from sample contamination.

Install

Pydamage is not yet on pypi nor conda, but you can already install it using pip, provided that you have access to this repository.

Install dependencies in conda environment

git clone [e-mail]:maxibor/pydamage.git
cd pydamage
conda env create -f environment.yml
conda activate pydamage

Install pydamage

• from source

python setup.py install

• from Github using pip

pip install git+ssh://[e-mail]/maxibor/pydamage.git

Documentation

pydamage.readthedocs.io

Help

$ 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: 20]
  -p, --process INTEGER  Number of processes  [default: 2]
  -m, --mini INTEGER     Minimum reads aligned to consider reference
                         [default: 2000]

  -c, --cov FLOAT        Minimum coverage to consider reference  [default:
                         0.5]

  -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