Metadata-Version: 2.1
Name: thapbi-pict
Version: 0.6.3
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 a sequence 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.
        
        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.
        
        Installation
        ------------
        
        We recommend installing this tool on Linux or macOS 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
        
        Sadly 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 Phyto-Threats project was supported from 2016 to 2019 under the Tree
        Health and Plant Biosecurity Initiative (THAPBI), jointly funded by the
        Biotechnology and Biological Sciences Research Council (`BBSRC
        <https://bbsrc.ukri.org/>`_), Department for Environment, Food and Rural
        affairs (`DEFRA <https://www.gov.uk/government/organisations/department-for-environment-food-rural-affairs>`_),
        Economic and Social Research Council (`ESRC <https://esrc.ukri.org>`_),
        `Forestry Commission <https://www.gov.uk/government/organisations/forestry-commission>`_,
        Natural Environment Research Council (`NERC <https://nerc.ukri.org>`_)
        and `Scottish Government <https://www.gov.scot/>`_.
        
        Background
        ----------
        
        THAPBI PICT 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 :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
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
