TCR Annotation¶

abstar fully supports T-cell receptor (TCR) sequence annotation using the --receptor tcr option.

Basic Usage¶

Command Line:

abstar run tcr_sequences.fasta output/ --receptor tcr

# Human TCR (default germline database)
abstar run tcr.fasta output/ --receptor tcr --germline_database human

# Mouse TCR
abstar run tcr.fasta output/ --receptor tcr --germline_database mouse

Python:

import abstar

# Annotate TCR sequences
sequences = abstar.run("tcr_sequences.fasta", receptor="tcr")

# Return as DataFrame
df = abstar.run("tcr_sequences.fasta", receptor="tcr", as_dataframe=True)

TCR Chain Types¶

abstar supports all TCR chain types:

Alpha chain (TRA): V and J gene segments
Beta chain (TRB): V, D, and J gene segments
Gamma chain (TRG): V and J gene segments
Delta chain (TRD): V, D, and J gene segments

D gene assignment applies only to beta and delta chains.

Available Germline Databases¶

TCR germline databases are available for:

human: Human TCR (alpha, beta, gamma, delta)
mouse: Mouse TCR (alpha, beta, gamma, delta)

Output Fields¶

TCR annotations include the same fields as BCR annotations:

Gene calls: v_call, d_call (beta/delta only), j_call
Regions: CDR1, CDR2, CDR3, FWR1-4
Mutations and quality metrics
Junction analysis

The locus field indicates the chain type (TRA, TRB, TRG, TRD).

Custom TCR Databases¶

Build custom TCR databases using build_germline_database:

Command Line:

abstar build_germline_database my_tcr_db \
    -f tcr_v_genes.fasta \
    -f tcr_d_genes.fasta \
    -f tcr_j_genes.fasta \
    --receptor tcr

Python:

import abstar

abstar.tl.build_germline_database(
    name="my_tcr_db",
    fastas=["tcr_v.fasta", "tcr_d.fasta", "tcr_j.fasta"],
    receptor="tcr"
)

Then use the custom database:

abstar run tcr.fasta output/ --receptor tcr --germline_database my_tcr_db

Differences from BCR Annotation¶

No isotype assignment: TCRs do not have isotypes, so c_call is not assigned for TCR sequences
D gene: Only beta and delta chains have D gene segments
Constant regions: TCR constant regions are not annotated