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:
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