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add support for multi-locus TRA/TRD detection in getLocus function #227

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Merged
ssnn-airr merged 1 commit into from
Jan 12, 2026
Merged

add support for multi-locus TRA/TRD detection in getLocus function #227

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7 changes: 7 additions & 0 deletions changeo/Gene.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
gene_regex = re.compile(r'((IG[HLK]|TR[ABGD])([VDJ][A-R0-9]+[-/\w]*))')
family_regex = re.compile(r'((IG[HLK]|TR[ABGD])([VDJ][A-R0-9]+))')
locus_regex = re.compile(r'(IG[HLK]|TR[ABGD])')
multi_locus_tra_trd = re.compile(r'TRAV\d+(?:-\d+)?/DV\d+')

v_allele_regex = re.compile(r'((IG[HLK]|TR[ABGD])V[A-R0-9]+[-/\w]*[-\*][\.\w]+)')
d_allele_regex = re.compile(r'((IG[HLK]|TR[ABGD])D[A-R0-9]+[-/\w]*[-\*][\.\w]+)')
Expand Down Expand Up @@ -115,6 +116,12 @@ def getLocus(gene, action='first'):
str: String of the first locus call when action is 'first'.
tuple: Tuple of locus calls for 'set' or 'list' actions.
"""
if multi_locus_tra_trd.search(gene):
dual = ['TRA', 'TRD']
if action == 'first':
return 'TRA/TRD'
elif action in ('set', 'list'):
return tuple(dual)
return parseGeneCall(gene, locus_regex, action=action)


Expand Down