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: 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 ]
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.
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/.
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- 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
- libcurl-devel
- g++
- python36
- R-devel
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.whlBoth 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
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