Metadata-Version: 2.1
Name: thapbi-pict
Version: 0.3.3
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
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
Requires-Dist: biopython
Requires-Dist: matplotlib
Requires-Dist: networkx
Requires-Dist: pydot
Requires-Dist: python-levenshtein
Requires-Dist: sqlalchemy
Requires-Dist: xlsxwriter

.. 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)
=================================================

THAPBI PICT an ITS1-based diagnostic/profiling tool from the UK
`BBSRC <https://www.bbsrc.ac.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.

The `tool documentation <https://thapbi-pict.readthedocs.io/>`_ is
hosted by `Read The Docs <https://readthedocs.org/>`_, generated
automatically from the ``docs/`` folder of the `software repository
<https://github.com/peterjc/thapbi-pict/>`_.

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


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.


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.


