A KBase module using the KBase SDK.
FastANI is a whole-genome similarity estimation utility. Refer to its documentation for more details about the algorithm.
This project uses Jinja2 for templating html/css. You can install pip dependencies locally with pipenv and the Pipfile
Note that kb-sdk test must be run against the CI environment, which has a hard coded
public workspace containing test data.
I have some manual unit tests that bypass the kb-sdk workflow to support TDD. To get these to run:
- Download and compile fastANI and place the executable in your PATH
- Install R and the genPlotR package
PYTHONPATH=lib python test/test_fast_ani.py
Instead of using fastANI's --rl and --ql parameters, I only run the binary on single genome files, mostly so we can generate visualizations and parallelize it. For multiple assemblies, I run the binary in parallel on every pair of assembly and generate a separate pdf visualization for every one.
Other notes:
- Running genome A as query and B as reference does not give equivalent results as running B for query and A for reference (ie. reversing parameters)
- Running with a query-list and reference-list that both have single genomes gives equivalent results to running a single query file to a single reference fie.
- The reference-list or query-list files should have paths relative to the directory in which you run the binary
FastANI has an R-based visualization of the genome similarities that has to get generated with genPlotR. It gets set up in the Dockerfile and run from python inside lib/fastANI/fast_ani_proc.py
MIT