Welcome to pydamage’s documentation!¶

Introduction¶

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 git@github.com: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://git@github.com/maxibor/pydamage.git

CLI help¶

Command line interface help message

pydamage --help

API¶

pydamage.main.analyze(bam, wlen=30, show_al=False, mini=2000, cov=0.5, process=1, outdir='', plot=False, verbose=False, force=False)[source]¶

Runs the pydamage analysis

Parameters:	bam (str) – Path to alignment (sam/bam/cram) file wlen (int) – window length show_al (bool) – print alignments representations mini (int) – Minimum numbers of reads aligned to consider contigs cov (float) – Minimum coverage to consider contig process (int) – Number of processes for parellel computing outdir (str) – Path to output directory verbose (bool) – verbose mode force (bool) – force overwriting of results directory
Returns:	pandas DataFrame containg pydamage results
Return type:	pd.DataFrame

CLI¶

To access the help menu:

$ pydamage --help

The list of arguments of options is detailed below

pydamage¶

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

pydamage [OPTIONS] BAM

Options

--version¶: Show the version and exit.

-w, --wlen <wlen>¶: Window length for damage modeling [default: 35]

-p, --process <process>¶: Number of processes [default: 2]

-m, --mini <mini>¶: Minimum reads aligned to consider reference [default: 1000]

-c, --cov <cov>¶: Minimum coverage to consider reference [default: 8]

-s, --show_al¶: Show alignments representations

-pl, --plot¶: Make the damage plots

--verbose¶: Verbose mode

-o, --outdir <outdir>¶: Output directory [default: pydamage_results]

--force¶: Force overwriting of results directory

Arguments

BAM¶: Required argument