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DNASnout client

Project description


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.


This installs as a regular Python package:

python install

Development version

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

# installation directory

# install
# 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 -O - | python
# install pip
easy_install pip
# install dependencies
#     numpy
pip install numpy
#     bitarray
pip install bitarray
#     ngs_plumbing
pip install
# install dnasnout-client
pip install
# installation is complete
# deactivate the virtualenv

Test the installation

# use the virtual environment
source ${INSTALLDIR_CLIENT}/dnasnoutclient_env/bin/activate
# download test data
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:


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

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