Metadata-Version: 2.1
Name: thapbi-pict
Version: 0.4.4
Summary: THAPBI Phytophthora ITS1 Classifier Tool (PICT).
Home-page: https://github.com/peterjc/thapbi-pict
Author: Peter Cock
Author-email: peter.cock@hutton.ac.uk
License: UNKNOWN
Download-URL: https://github.com/peterjc/thapbi-pict
Description: .. image:: https://img.shields.io/pypi/v/thapbi_pict.svg
           :alt: THAPBI PICT on the Python Package Index (PyPI)
           :target: https://pypi.org/project/thapbi-pict/
        .. image:: https://img.shields.io/conda/vn/bioconda/thapbi-pict.svg
           :alt: THAPBI PICT on BioConda
           :target: https://anaconda.org/bioconda/thapbi-pict
        .. image:: https://img.shields.io/travis/peterjc/thapbi-pict/master.svg?label=master&logo=travis
           :alt: THAPBI PICT TravisCI build status
           :target: https://travis-ci.org/peterjc/thapbi-pict/branches
        .. image:: https://img.shields.io/circleci/project/github/peterjc/thapbi-pict/master.svg?label=master&logo=CircleCI
           :alt: THAPBI PICT CircleCI build status
           :target: https://circleci.com/gh/peterjc/thapbi-pict/tree/master
        .. image:: https://img.shields.io/readthedocs/thapbi-pict.svg?logo=read-the-docs
           :alt: Documentation Status
           :target: https://readthedocs.org/projects/thapbi-pict/builds/
        .. image:: https://img.shields.io/badge/code%20style-black-000000.svg
           :alt: Code style: black
           :target: https://github.com/python/black
        
        THAPBI *Phytophthora* ITS1 Classifier Tool (PICT)
        =================================================
        
        About
        -----
        
        THAPBI PICT is an ITS1-based diagnostic/profiling tool from the UK funded Tree
        Health and Plant Biosecurity Initiative (THAPBI) `Phyto-Threats project
        <https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/>`_,
        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.
        
        Installation
        ------------
        
        We recommend installing this tool on Linux using the
        `Conda <https://conda.io/>`__ packaging system, via the
        `BioConda <https://bioconda.github.io/>`__ channel, which will handle
        *all* the dependencies:
        
        .. code:: console
        
           $ 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) <https://pypi.python.org/>`__, the following command will install
        it along with its Python dependencies:
        
        .. code:: console
        
           $ 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.
        
        Quick Start
        -----------
        
        Once installed, you should be able to run the tool at the command line
        using:
        
        .. code:: console
        
           $ 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.
        
        Documentation
        -------------
        
        The `tool documentation <https://thapbi-pict.readthedocs.io/>`_ is hosted by
        `Read The Docs <https://readthedocs.org/>`_, generated automatically from the
        ``docs/`` folder.
        
        Funding
        -------
        
        The THAPBI Phyto-Threats project is supported by a grant funded jointly by the
        Biotechnology and Biological Sciences Research Council (`BBSRC
        <https://bbsrc.ukri.org/>`_), the Department for Environment, Food and Rural
        affairs (`DEFRA <https://www.gov.uk/government/organisations/department-for-environment-food-rural-affairs>`_),
        the Economic and Social Research Council (`ESRC <https://esrc.ukri.org>`_),
        the `Forestry Commission <https://www.gov.uk/government/organisations/forestry-commission>`_,
        the Natural Environment Research Council (`NERC <https://nerc.ukri.org>`_)
        and the `Scottish Government <https://www.gov.scot/>`_, under the Tree
        Health and Plant Biosecurity Initiative (THAPBI).
        
        Background
        ----------
        
        This 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
        
        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.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: Freely Distributable
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.5
Description-Content-Type: text/x-rst
