clonotypes: Implement --clustered option and allow multiple input tables

NBISweden / IgDiscover-legacy

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads

https://www.igdiscover.se

MIT License

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clonotypes: Implement --clustered option and allow multiple input tables #119

Closed marcelm closed 10 months ago

marcelm commented 2 years ago

This works quite similar to the clonoquery subcommand, but it allows querying multiple reference tables, which are simply merged into one table before querying. For now, this is a separate subcommand because the order of arguments needed to change: clonoquery expects reference, then query, but since clonoquery2accepts multiple references, the order for that command is query, then reference (plus more references).

To Do

[x] Output a "members" table even if --clustered is provided
[x] Make --clustered output contain all the AIRR columns

rodrigarc commented 2 years ago

Hi Marcel, but if it is doing exactly what the normal clonoquery does, wouldn't we have the same problem of misrepresenting clonal sizes?

Is it using only one reference sequence from each clonotype to be queried?
How is it considering a bulk sequence that is part of the same clonotype on bulk but is not similar enough to the queried sequence?

marcelm commented 2 years ago

This is just a starting point (note that I marked the PR as draft). The intention is to reproduce the querying method that you implemented in your two R scripts. (It will probably be closer to the clonotypes command at that stage.)

marcelm commented 10 months ago

This repository is outdated and is going to be archived. Please see the new repository at https://gitlab.com/gkhlab/igdiscover22/ or the homepage at https://www.igdiscover.se/ for the most recent and maintained IgDiscover version.