A repository for QIIME example input and output

26 07 2012

Hello QIIME users,

We’ve recently begun assembling a repository of example input and output files for use with QIIME. You can find this in our GitHub repository here:


The repository has been moved to: https://github.com/qiime/qiime_test_data.

This repository currently contains example input and output for around 30% of QIIME’s scripts, and we’ll be continuing to add more example input and output over the next few months. You can find the example input and output for a script by looking up the script name in the repository at the link above. For example, example input and output for filter_samples_from_otu_table.py in the filter_samples_from_otu_table directory in the qiime_test_data repository. Note that the example input and output files correspond to the usage examples that you see when you call a script with it’s -h parameter or on the script’s documentation page (e.g., filter_samples_from_otu_table.py), so you can see exactly how to use the script and try it out for yourself.

This repository is designed to serve a few purposes. First, it’s an additional source of documentation. For example, if you’re trying to assemble data for use with QIIME you can review the corresponding example input to see what your files should look like. You can also use it for debugging: if a QIIME script is failing, you can test the script with the example data from the qiime_test_data repository to confirm that the script is working correctly with input that you know is valid. Next, the QIIME development group uses this for automated testing. In the repository you’ll see a script_usage_tests.py file. We run this (call it with the -h parameter to see how) to confirm that all of the script interfaces are currently working with example input. This has historically been hard for us to do in QIIME, and this new script testing framework will help keep QIIME more stable. This can also be run via Qiime/tests/all_tests.py by adding the qiime_test_data_dir to your .qiime_config file: in that case, every time you run all_tests.py, the interfaces for the scripts will be tested in addition to the full unit test suite.

Get in touch on the QIIME forum with any questions.





One response

19 12 2012
QIIME 1.6.0 is live! « QIIME News and Announcements

[…] Building from the recent development of the qiime_test_data repository (as discussed here), which contains example input and output for most QIIME scripts, the script documentation was […]

%d bloggers like this: