thapbi-pict 0.3.1

THAPBI Phytophthora ITS1 Classifier Tool (PICT).

THAPBI Phytophthora ITS1 Classifier Tool (PICT)

THAPBI PICT an ITS1-based diagnostic/profiling tool from the UK BBSRC funded Tree Health and Plant Biosecurity Initiative (THAPBI) Phyto-Threats project, focused on identifying Phytophthora species present in Illumina sequenced environmental samples.

Phytophthora (from Greek meaning plant-destroyer) species are economically important plant pathogens, important in both agriculture and forestry. ITS1 is short for Internal Transcribed Spacer one, which is a region of eukaryotes genomes between the 18S and 5.8S rRNA genes. This is commonly used for molecular barcoding, where sequencing this short region can identify species.

This software repository continues earlier work including:

• https://github.com/widdowquinn/THAPBI

• https://github.com/widdowquinn/THAPBI-pycits

• https://github.com/peterthorpe5/THAPBI-pycits

• https://github.com/peterthorpe5/public_scripts/tree/master/metapy

• https://github.com/peterthorpe5/public_scripts/tree/master/metapy_tools

Installation

We recommend installing this tool on Linux using the Conda packaging system, via the BioConda channel, which will handle all the dependencies:

$ conda install thapbi_pict

The same should work on macOS, but the command line dependencies likely rule out using Windows directly.

Alternatively, since the software is on the Python Package Index (PyPI), the following command will install it along with its Python dependencies:

$ pip install thapbi_pict

However, in this case you will still need to install various external command line tools like hmmer, and others which are only used for some classifiers (like blast and swarm). If you have BioConda setup, use the following:

$ conda install --file requirements-ext.txt

On a typical Linux system most of the tools required will be available via the default distribution packages, although not always under the same package name.

On Debian (with the efforts of DebianMed), or Ubuntu Linux, try:

$ sudo apt-get install ncbi-blast+ cutadapt hmmer swarm trimmomatic

If you want to install the very latest unreleased code, you must download the source code from GitHub - see the CONTRIBUTING.rst file for more details.

Once installed, you should be able to run the tool using:

$ thapbi_pict

This should automatically find the installed copy of the Python code. Use thapbi_pict -v to report the version, or thapbi_pict -h for help.

Release History

See the CHANGELOG.rst file (it was getting too long to include here).

Development Notes

Please see the CONTRIBUTING.rst file for details of the development setup including Python style conventions, git pre-commit hook, continuous integration and test coverage, and release process.