THAPBI Phytophthora ITS1 Classifier Tool (PICT).
THAPBI Phytophthora ITS1 Classifier Tool (PICT)
THAPBI PICT is a sequence based diagnostic/profiling tool from the UK 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.
With appropriate primer and HMM settings, and a custom database, THAPBI PICT can be applied to other organisms and/or barcode marker sequences - not just ITS1.
$ conda install thapbi_pict
Sadly 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. See INSTALL.rst for more details, and if you want to modify the software read CONTRIBUTING.rst as well.
Once installed, you should be able to run the tool at the command line using:
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.
The THAPBI Phyto-Threats project is supported by a grant funded jointly by the Biotechnology and Biological Sciences Research Council (BBSRC), the Department for Environment, Food and Rural affairs (DEFRA), the Economic and Social Research Council (ESRC), the Forestry Commission, the Natural Environment Research Council (NERC) and the Scottish Government, under the Tree Health and Plant Biosecurity Initiative (THAPBI).
This continues earlier work including:
See the CHANGELOG.rst file (it was getting too long to include here).
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.
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