BenTenmann/setriq-service

setriq-service

The functionalities of setriq provided as a Seldon service in a Helm chart. Assuming a running Kubernetes cluster, the service can be installed by running the following in the root of this repository:

helm install `basename $PWD` helm/

Pairwise distances can then be computed by running the following:

# port forward service
kubectl port-forward svc/`basename $PWD` 9000 &

# send post request for a batch of sequences
curl -X POST localhost:9000/api/v1.0/predictions \
    -H 'Content-Type: application/json' \
    -d '{"sequences": ["CASSLKPNTEAFF", "CASSAHIANYGYTF", "CASRGATETQYF"]}'

This will return a JSON object with a single field distances, which is a JSON array of floats. In this case, this array will be of length 3, as $n \times \frac{n - 1}{2} = 3$, where $n$ is the number of sequences.

The distances returned in this case are Levenshtein distances. This is because this is the default metric of the service (defined in setriq_service/default_metric_spec.json). However, any of the distance functions implemented in setriq can be used, simply by specifying the spec field in the POST request:

curl -X POST localhost:9000/api/v1.0/predictions \
     -H 'Content-Type: application/json' \
     -d '{
            "sequences": ["CASSLKPNTEAFF", "CASSAHIANYGYTF", "CASRGATETQYF"],
            "spec": {"id": "CdrDist", "param": {"gap_opening_penalty": 5.0, "gap_extension_penalty": 2.0}}
     }'

Here we have specified the distance function to be CdrDist with the custom parameters under the param field. Note that the param field is optional, as long as the corresponding class from setriq does not require those parameters at initialisation.