Supported parameters NCBI BLAST API

[comatrion]

There seem to be some parameters supported in the biogo blast interface e.g. PERC_IDENT that are not supported (or 'should not be relied upon') according to the NCBI's documentation https://ncbi.github.io/blast-cloud/dev/api.html. Is this the correct documentation relevant to the biogo interface or has there been some change?

[kortschak]

Thank you for the report. bíogo development is currently unfunded and so fixes and improvements are provided on a best effort basis.

Having said that, a way forward for this would be to take this opportunity to migrate from XML serialisation, add in the additional blast result records components that were added a while back and so leave v1, moving to biogo/ncbi v2. I'd be very happy for the XML stuff to go away. I will not be likely to get to do this anytime soon, but will review PRs.

[kortschak]

@peterjc Do you have a pointer to where the BLAST+ "Single-file BLAST JSON" (--outfmt=15) spec lives?

[peterjc]

No, but it would be worth emailing the blast team and asking if you can't find this in the online docs.

[kortschak]

The only data schema descriptions are XSD and DTD here. They have nothing nice, but I imagine that the JSON will conform to the XML as much as it in principle can.

[kortschak]

From NLM support:

We do not have JSON specs. Checking with our developers, the JSON output is based on the XML output and for that you already know where the DTDs are.

Our C++ document contains a json wrapper section, which may be of some additional help:
https://ncbi.github.io/cxx-toolkit/pages/ch_jsonwrapp