Metadata-Version: 1.1
Name: gaet
Version: 0.3.0
Summary: Evaluate the quality of a genome assembly based on annotated genes
Home-page: https://gitlab.com/michaelbarton/gaet/
Author: Michael Barton
Author-email: mail@michaelbarton.me.uk
License: BSD
Description: GAET
        ====
        
        Gene-based assembly evaluation tool - evaluate a single assembly or
        compare two assemblies using their annotations.
        
        Getting Started
        ---------------
        
        ::
        
            pip install [--user] gaet
        
            gaet assembly.gff
            gaet --reference reference.gff assembly.gff
        
        Gaet is written in python 3. If you would prefer, there is a `precompiled
        version of gaet`_ which runs on Linux systems.
        
        .. _precompiled version of gaet: https://s3-us-west-1.amazonaws.com/gaet/releases/latest.tar.xz
        
        Documentation
        -------------
        
        See `gaet(1)`_ for a description of how to run gaet. See `gaet-format(5)`_
        for a description of the output metrics generated by gaet.
        
        .. _gaet(1): https://gitlab.com/michaelbarton/gaet/blob/master/doc/src/gaet.1.md
        .. _gaet-format(5): https://gitlab.com/michaelbarton/gaet/blob/master/doc/src/gaet-format.5.md
        
        Running the tests
        -----------------
        
        Gaet has both unit tests and feature tests. The unit tests check individual
        python functions within the code. The feature tests are run against the
        compiled version of gaet and ensure the program works as a whole.
        
        ::
        
            make test
            make feature
        
        Upon a successful pull request onto the master branch, where all tests
        pass, a new version of gaet will be released to pypi, and a new precompiled
        version released to S3.
        
        Built With
        ----------
        
        -  `funcy <https://pypi.python.org/pypi/funcy>`__ - functional
           programming for python
        -  `gffutils <https://pypi.python.org/pypi/gffutils>`__ - Utilities for
           accessing GFF data
        -  `pyfaidx <https://pypi.python.org/pypi/pyfaidx>`__ - Accessing
           substrings of FASTA data
        -  `ruamel.yaml <https://pypi.python.org/pypi/ruamel.yaml>`__ - actively
           maintained YAML parsing for python
        
        Authors
        -------
        
        -  `Michael Barton <http://michaelbarton.me.uk>`__
        
        License
        -------
        
        This project is licensed under the BSD License - see the
        `LICENSE.txt <LICENSE.txt>`__ file for details.
        
        See also
        --------
        
        -  `QUAST <http://quast.sourceforge.net/>`__- check the completeness of
           an assembly or compare with a reference using size metrics such
           nga50.
        
        -  `checkm <http://ecogenomics.github.io/CheckM/>`__ - checks the
           completeness of an assembly using the expectation of certain
           essential genes.
        
Keywords: genomics bioinformatics sequencing assembly
Platform: UNKNOWN
Classifier: License :: OSI Approved :: BSD License
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
