pRESTO style annotations and IgBlast AIRR output

[schristley]

I've been working with IgBlast 1.12 on VDJServer to produce AIRR output. One thing I noticed is that pRESTO style annotations in the sequence_id are not handled, such as:

M01375:31:000000000-A75VU:1:1105:24713:12796|DUPCOUNT=1

With ChangeO, when it parsed IgBlast output, it would pull out those annotations and make them a column in the AIRR TSV (DUPCOUNT -> duplicate_count). Thankfully IgBlast doesn't trim the sequence_id so those annotations seem to be there in the AIRR TSV output.

How should we handle this now? Should we add support into (say) airr-tools to do this, or should we consider this "outside" of AIRR, and thus ChangeO should provide a mechanism (I can easily write my own script to do it too)?

[javh]

I'm inclined to say this is outside the scope of the airr package and something that should be part of changeo.

I unfortunately haven't had time to work on changeo recently, but this is probably something we should incorporate into the unfinished IMGT numbering command in ConvertDb. So there would be one command in changeo to parse the airr fields to pull out presto annotations and insert IMGT numbering spacers. (Ie, a simple parser for igblast --outfmt 19 data.)

[schristley]

out of scope