Metadata-Version: 2.1
Name: bionorm
Version: 0.2.1
Summary: normalize and verify genomic data
Home-page: https://github.com/ncgr/ncgr
Keywords: science,biology,bioinformatics,genomics,data science,DNA,protein,sequences,FASTA,GFF,curation,wrangling
Author: Connor Cameron
Author-email: ctc@ncgr.org
Maintainer: Joel Berendzen
Maintainer-email: joelb@ncgr.org
Requires-Python: >=3.6,<4.0
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: biopython (>=1.76,<2.0)
Requires-Dist: click (>=7.0,<8.0)
Requires-Dist: click_plugins (>=1.1.1,<2.0.0)
Requires-Dist: coverage (>=5.0.3,<6.0.0)
Requires-Dist: importlib_metadata (>=1.5.0,<2.0.0)
Requires-Dist: ruamel.yaml (>=0.16.6,<0.17.0)
Requires-Dist: sequencetools (>=0.0.5,<0.0.6)
Project-URL: Documentation, https://bionorm.readthedocs.org
Description-Content-Type: text/x-rst

bionorm
=======
normalize and validate genomic data files

Prerequisites
-------------
Python 3.6 or greater is required.


Installation
------------
This package is tested under Linux and MacOS using Python 3.7.
Install via pip, pipx, or pipenv in the usual way: ::

     pipx install bionorm

Developers
----------
bionorm uses the `poetry <https://python-poetry.org>` dependency manager.
Install poetry in the usual way.  Get the version of python you intend
to use as first in the path, and execute the command: ::

    curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python

Next, get the master branch from GitHub ::

	git clone https://github.com/ncgr/bionorm.git

Change to the bionorm/ directory and install with poetry: ::

	poetry install -v

Run bionorm with poetry: ::
    poetry run bionorm

Usage
-----
Installation puts a single script called ``bionorm`` in your path.  The usage format is::

    bionorm [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS] [ARGS]

A listing of commands is available via ``bionorm --help``.  Current available commands are:

============================= ====================================================
  busco                       Perform BUSCO checks.
  detector                    Detect/correct incongruencies among files.
  fasta                       Check for GFF/FASTA consistency.
  generate_readme             Generates a README file with details of genome.
  index                       Indexes FASTA file.

============================= ====================================================


+-------------------+------------+------------+
| Latest Release    | |pypi|     | |bionorm|  |
+-------------------+------------+            +
| GitHub            | |repo|     |            |
+-------------------+------------+            +
| License           | |license|  |            |
+-------------------+------------+            +
| Documentation     | |rtd|      |            |
+-------------------+------------+            +
| Travis Build      | |travis|   |            |
+-------------------+------------+            +
| Coverage          | |coverage| |            |
+-------------------+------------+            +
| Code Grade        | |codacy|   |            |
+-------------------+------------+            +
| Dependencies      | |depend|   |            |
+-------------------+------------+            +
| Issues            | |issues|   |            |
+-------------------+------------+------------+


.. |bionorm| image:: docs/normal.jpg
     :alt: Make me NORMAL, please!

.. |pypi| image:: https://img.shields.io/pypi/v/bionorm.svg
    :target: https://pypi.python.org/pypi/bionorm
    :alt: Python package

.. |repo| image:: https://img.shields.io/github/commits-since/ncgr/bionorm/0.1.svg
    :target: https://github.com/ncgr/bionorm
    :alt: GitHub repository

.. |license| image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
    :target: https://github.com/ncgr/bionorm/blob/master/LICENSE.txt
    :alt: License terms

.. |rtd| image:: https://readthedocs.org/projects/bionorm/badge/?version=latest
    :target: http://bionorm.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Server

.. |travis| image:: https://img.shields.io/travis/ncgr/bionorm.svg
    :target:  https://travis-ci.org/ncgr/bionorm
    :alt: Travis CI

.. |codacy| image:: https://api.codacy.com/project/badge/Grade/b23fc0c167fc4660bb649320e14dac7f
    :target: https://www.codacy.com/gh/ncgr/bionorm?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=ncgr/bionorm&amp;utm_campaign=Badge_Grade
    :alt: Codacy.io grade

.. |coverage| image:: https://codecov.io/gh/ncgr/bionorm/branch/master/graph/badge.svg
    :target: https://codecov.io/gh/ncgr/bionorm
    :alt: Codecov.io test coverage

.. |issues| image:: https://img.shields.io/github/issues/ncgr/bionorm.svg
    :target:  https://github.com/ncgr/bionorm/issues
    :alt: Issues reported

.. |depend| image:: https://api.dependabot.com/badges/status?host=github&repo=ncgr/bionorm
     :target: https://app.dependabot.com/accounts/ncgr/repos/236847525
     :alt: dependabot dependencies


