Evaluate the quality of a genome assembly based on annotated genes
Project description
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.
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.
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 - functional programming for python
gffutils - Utilities for accessing GFF data
pyfaidx - Accessing substrings of FASTA data
ruamel.yaml - actively maintained YAML parsing for python
License
This project is licensed under the BSD License - see the LICENSE.txt file for details.
See also
Project details
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