AIRR mapping#

vdjdb convert airr emits AIRR Rearrangement, Receptor and Reactivity from the definitive tables. The mapping below is declared once, on the field registry, and both converters - new-format and legacy - read it from there.

An empty mapping means that no AIRR field holds the same quantity, not that no related field exists. VDJdb’s v.end is an amino-acid offset in junction space, while AIRR’s v_sequence_end is a nucleotide offset in sequence space. vdjdb.convert.coords is the only module that converts between the four coordinate spaces used in this codebase.

  • antigen.epitope -> peptide_sequence_aa

  • antigen.gene -> antigen

  • antigen.species -> antigen_source_species

  • cdr3 -> junction_aa

  • cdr3nt -> junction

  • d.inferred -> d_call

  • d.segm -> d_call

  • gene -> locus

  • j.segm -> j_call

  • mhc.a -> mhc_allele_1

  • mhc.b -> mhc_allele_2

  • mhc.class -> mhc_class

  • reference.id -> reactivity_refs

  • v.segm -> v_call

  • vdjdb.score -> reactivity_value

Species vocabulary#

  • HomoSapiens

  • MacacaMulatta

  • MusMusculus

  • RattusNorvegicus

Declared tables#

  • chains

  • chunk

  • cluster_members

  • epitopes

  • evidence

  • full

  • motif_pwms

  • records

  • restriction

  • slim

  • vdjdb

  • vdjdb-web