writeChangeoDb() puts NA for null/blank values

[Scott Christley]

I’m using the immcantation/suite:4.1.0 docker images. I read in an AIRR TSV file which has null/blank values for some field, calculate AA properties then write a new AIRR TSV file. The resultant file has NA for those fields and the file fails validation.

db <- readChangeoDb("/data/test/vdjserver1.airr.tsv")
d <- aminoAcidProperties(db)
writeChangeoDb(d, "new.airr.tsv")


$ airr-tools validate rearrangement -a new.airr.tsv 
Validating: new.airr.tsv
new.airr.tsv at record 1 has validation error: field complete_vdj has invalid bool NA
new.airr.tsv at record 2 has validation error: field complete_vdj has invalid bool NA
new.airr.tsv at record 3 has validation error: field complete_vdj has invalid bool NA
new.airr.tsv at record 4 has validation error: field complete_vdj has invalid bool NA

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[Jason Vander Heiden]

Try with airr::read_rearrangement and airr::write_rearrangement instead. The read/write changeo functions are for the legacy changeo format.

[Scott Christley]

Ok, thanks, that works. It might helpful to point users to that in the documentation, for example in the Package Overview it give the changeo functions for file i/o which leads the user to think that they should be used. But maybe you have a separate issue for that, and you can close this one. All the vignettes use the exampledb, so there isn’t an example of reading/writing AIRR TSV files.

[Jason Vander Heiden]

Yeah, that’s a good point. We’ll figure out a way to clarify that in the documentation. The rearrangement IO functions aren’t in alakazam, so they aren’t appropriate to add to the package overview, but we’ll figure something out.

[Jason Vander Heiden]

Documentation issue. Opened a separate issue.