Contatester

Contatester computes the Allelic Balance of a sample from a VCF file, check if a cross human contamination is present and estimate the degree of contamination, using pegasus for high efficiency

Usage

usage: contatester [options]

Detection and determination of the presence of cross contaminant

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  VCF file version 4.2 to process. If -f is used don't
                        use -l (Mandatory)
  -l LIST, --list LIST  input text file, one vcf by lane. If -l is used don't
                        use -f (Mandatory)
  -o OUTDIR, --outdir OUTDIR
                        folder for storing all output files (optional)
                        [default: current directory]
  -e EXPERIMENT, --experiment EXPERIMENT
                        Experiment type, could be WG for Whole Genome or EX
                        for Exome [default WG]
  -r, --report          create a pdf report for contamination estimation
                        [default: no report]
  -c, --check           enable contaminant check for each VCF provided if a
                        VCF is marked as contaminated
  -m MAIL, --mail MAIL  send an email at the end of the job
  -A ACCOUNTING, --accounting ACCOUNTING
                        msub option for calculation time imputation
  -d DAGNAME, --dagname DAGNAME
                        DAG file name for pegasus
  -t THREAD, --thread THREAD
                        number of threads used by job(optional) [default if
                        check enable|disable: 4|1]
  -s THRESHOLD, --threshold THRESHOLD
                        Threshold for contaminated status(optional) [default:
                        4 ]

Installation using Docker

To ease the use of contatester we provide a docker image. Example to get Contatester version 1.0.0 in few commands:

Get the contatester image

$ docker pull cnrgh/contatester:1.0.0

Run a container using our image

$ docker run --rm \
             --name="contatester" \
             --volume "$(pwd)/my_data":/data \
             --volume "$(pwd)/my_out_dir":result_dir \
             cnrgh/contatester:1.0.0 -f /data/test_1.vcf.gz -o /result_dir

Here we create a container named contatester using the image cnrgh/contatester:1.0.0.

The directory my_data is mount bind into the container to /data and my_out_dir to /result.

The contatester application is executed with parameters -f and -o.

Results are stored both into result for the container and $(pwd)/my_out_dir for the host.

License

Contatester is released under the terms of the CeCILL license, a free software license agreement adapted to both international and French legal matters that is fully compatible with the GNU GPL, GNU Affero GPL and/or EUPL license.

For further details see LICENSE file or check out https://cecill.info/.

How to contribute ?

In order to test your application and all dependencies are well declared, you have to create a virtual env

$ python3 -m venv linux_venv
$ source linux_venv/bin/activate

Dependencies

Runtime

python >= 3.6
python libraries : pathlib, os, typing, argparse, io, subprocess, sys, glob, datetime
R 3.3.1
R libraries : optparse, grid, gridBase, gridExtra
bcftools >= 1.9
pegasus >= 4.8.2

Build time

libcurl-devel
g++
python36
R-devel

Local Installation

Build

We are using setuptools as software build tool. In order to build this project, you have to run:

$ pip install --upgrade pip wheel setuptools
$ python setup.py bdist_wheel

$ pip install dist/contatester-1.0.0-py2.py3-none-any.whl

Clean

Both setuptools and distutils commands are extended to ensure that all cache files are cleaned. Indeed python generate *.pyc, *.pyo file to store corresponding bytecode. These bytecode files are not always regenerated which could lead to some problems when working on a cross-environment (Windows <-> Linux). The extended clean command remove either __pycache__, *.egg-info, .eggs, .pytest_cache

Code quality

Any new python project need to:

Be compatible python 3.6 or higher
Use Typing see pep 484 and its documentation
Own a wide range of tests

This project include:

A framework to test various use cases and unit tests (pytest)
A code coverage tools (coverage.py)

You have to run python setup.py coverage before each production release and most of other times. These tools generate html reports into the directory htmlcov

CNRGH/contatester