distToNearest amino acid model – "IUPAC base expected" error

[Dasha Balashova]

Hello,

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Using distToNearest function (with immcantation/suite devel docker image) model=”aa” I have an error: task failed - "IUPAC base expected". Small data subsample (AA sequences correspond to IUPAC alphabet), code and error are attached.

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Best regards,

Dasha

[Jason Vander Heiden]

Greetings @Dasha Balashova ,

Sorry for the slow reply and thank you for the reproducible example.

distToNearest expects nucleotide sequence input even for the animo acid model. It does the translation automatically before calculating the distances. If you use the cdr3 column instead of the cdr3_aa column, then it should work. Meaning:

dist_ham <- distToNearest(data, sequenceColumn="cdr3", 
                          vCallColumn="v_call", jCallColumn="j_call",
                          model="aa", normalize="len", nproc=8)

That error is specifically coming from:

x <- data$cdr3_aa[1]
seqinr::translate(unlist(strsplit(x, "")), ambiguous=T)

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[ssnn]

This issue seems resolved and is not active. Reopen if needed.

[Dasha Balashova]

Dear Jason Vander Heiden,

thanks for the clarification.

Best regards,

Dasha