Overview

Read more about these tools (and see examples of input files) in the usage overview or watch a short introduction screencast.

Recoding allele names

This version of uniformate also performs data transliteration (recoding) when an optional transliteration file is provided.
Substitution files are one column lists of old_allele – new_allele, where new_allele can be a abridged UNIFORMAT allele expression:

allele or allele&allele or ...

Substitutions related to different loci are grouped under the LOCUS keyword, and the keyword for each locus is mandatory even if a given locus is not being changed (see example below where LOCUS 2 does not contain substitution rules):

# Example substitution file
LOCUS 1
A*01:01:01 - A*01:01
A*02 - A*02:01&A*02:02&A*02:03

# note no substitution data below 
LOCUS 2

LOCUS 3
C*01:02 - C*01
C*01:03 - C*01
null - C*01:02&null

Validation of allele names

This version of uniformate also performs validation of allele names either against the current verison of the IMGT/HLA nomenclature, either against a user supplied nomenclature file.
Nomenclature files are either old version of the official nomenclature, or files that are similar json two values files (only the second element taken as a valid name) or, more simply, one column lists of allele names (all loci confunded) as shown below.

# Example simple nomenclature file
A*01:01
A*01:02
A*02
## more lines [suppressed in this exemple]
## allele can be defined at very different levels and even be redundant
## order is not important
DRB1*123:456:789
## valid allele names do not need to be HLA names
DiseaseMarker
NonDisease