Metadata-Version: 2.1
Name: thapbi_pict
Version: 0.12.6
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
Project-URL: Documentation, https://thapbi-pict.readthedocs.io/
Project-URL: Source, https://github.com/peterjc/thapbi-pict/
Project-URL: Tracker, https://github.com/peterjc/thapbi-pict/issues
Description: .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4529395.svg
           :alt: Zenodo DOI
           :target: https://doi.org/10.5281/zenodo.4529395
        .. image:: https://img.shields.io/github/license/peterjc/thapbi-pict.svg?label=License
           :alt: MIT License
           :target: https://github.com/peterjc/thapbi-pict/blob/master/LICENSE.rst
        .. image:: https://results.pre-commit.ci/badge/github/peterjc/thapbi-pict/master.svg
           :target: https://results.pre-commit.ci/latest/github/peterjc/thapbi-pict/master
           :alt: pre-commit.ci status
        .. image:: https://img.shields.io/circleci/project/github/peterjc/thapbi-pict/master.svg?label=CI&logo=CircleCI
           :alt: CircleCI status
           :target: https://circleci.com/gh/peterjc/thapbi-pict/tree/master
        .. image:: https://img.shields.io/appveyor/ci/peterjc/thapbi-pict/master.svg?logo=appveyor
           :alt: AppVeyor status
           :target: https://ci.appveyor.com/project/peterjc/thapbi-pict/history
        .. image:: https://img.shields.io/readthedocs/thapbi-pict.svg?label=RTD&logo=read-the-docs
           :alt: Documentation Status
           :target: https://readthedocs.org/projects/thapbi-pict/builds/
        .. image:: https://img.shields.io/pypi/v/thapbi_pict.svg?label=PyPI
           :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?label=Bioconda
           :alt: THAPBI PICT on BioConda
           :target: https://anaconda.org/bioconda/thapbi-pict
        .. 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/>`_,
        initially focused on identifying *Phytophthora* species present in Illumina
        sequenced environmental samples.
        
        *Phytophthora* (from Greek meaning plant-destroyer) species are economically
        important plant pathogens, 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 settings and a custom database of full length markers,
        THAPBI PICT can be applied to other organisms and/or barcode marker sequences
        - not just *Phytophthora* ITS1. It requires overlapping paired-end Illumina
        reads which can be merged to cover the *full* amplicon marker. Longer markers
        or fragmented amplicons are not supported. Internally it works by tracking
        unique amplicon sequence variants (ASVs), using MD5 checksums as identifiers.
        
        The worked examples include oomycetes, fungi, fish, bats, and plants, and
        cover markers in ITS1, ITS2, 12S, 16S, COI, and more. The main criteria has
        been mock communities with known species composition.
        
        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
        
        Alternatively or on Windows, since `the software is on the Python Package
        Index (PyPI) <https://pypi.org/project/thapbi-pict/>`__, 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 (especially for Windows),
        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.
        
        The documentation includes more detailed discussion of the sample datasets
        in the ``examples/`` folder (which are based on published datasets).
        
        Funding
        -------
        
        The initial work was supported from 2016 to 2019 under the Tree Health and
        Plant Biosecurity Initiative (THAPBI) Phyto-Threats project:
        
          This research was supported by a grant funded jointly 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/>`_, under the Tree
          Health and Plant Biosecurity Initiative, grant number ``BB/N023463/1``.
        
        Work from 2020 to 2021 was supported in part under the *Early detection of
        Phytophthora in EU and third country nurseries and traded plants (ID-PHYT)*
        Euphresco project:
        
          Funded by DEFRA as part of the Future Proofing Plant Health project in
          support of Euphresco ID-PHYT.
        
        
        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.
        
        Development Notes
        -----------------
        
        See file ``CONTRIBUTING.rst`` 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: >=3.6
Description-Content-Type: text/x-rst
