Skip to main content

DNASnout client

Project description

About

This script comes in support of the submitted paper:

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

  • It requires:

    • Python 3.3 (note the “.3”)
    • bowtie2 (parameter “-a”, try “–help”)
  • It is self-documented (try “-h” or “–help”).

  • It is working on FASTQ or gzipped-FASTQ files, possibly on BAM files

Be gentle and please do not hammer the server like there is no tomorrow.

The latest released versions of the package will always be on Pypi.

Usage

This installs as a regular Python package:

python setup.py install

Development version

The following BASH lines show to install a development version in a virtual environment

# installation directory
INSTALLDIR_CLIENT=./installclient_dir

# install
mkdir -p ${INSTALLDIR_CLIENT}
# create a virtual environment (Python 3.3)
# (if 3.3 is the only Python on your system, `pyvenv` will be enough)
pyvenv-3.3 ${INSTALLDIR_CLIENT}/dnasnoutclient_env

# use the virtual environment
source ${INSTALLDIR_CLIENT}/dnasnoutclient_env/bin/activate

# Install packages
# bootstrap virtualenv
wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py -O - | python
# install pip
easy_install pip
# install dependencies
#     numpy
pip install numpy
#     bitarray
pip install bitarray
#     ngs_plumbing
pip install https://bitbucket.org/lgautier/ngs_plumbing/get/default.tar.gz
# install dnasnout-client
pip install https://bitbucket.org/lgautier/dnasnout-client/get/default.tar.gz
# installation is complete
# deactivate the virtualenv
deactivate

Test the installation

# use the virtual environment
source ${INSTALLDIR_CLIENT}/dnasnoutclient_env/bin/activate
cd ${INSTALLDIR_CLIENT}
# download test data
wget http://tapir.cbs.dtu.dk/static/iontorrent_head400.fq
python -m dnasnout_client.console -i iontorrent_head400.fq -d iontorrent_test

The module can be run directly:

python -m dnasnout_client.console

Help is available with:

python -m dnasnout_client.console –help

Oh, and here is a screenshot:

Screenshot

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

dnasnout-client-0.2.0.tar.gz (24.0 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page