Output Formats

abstar outputs annotations in AIRR-compatible format. Two file formats are supported:

• airr: Tab-delimited TSV file with header row

• parquet: Columnar binary format, more space-efficient for large datasets

Specifying Output Format

Command Line:

# Default: AIRR TSV
abstar run sequences.fasta output/

# Parquet format
abstar run sequences.fasta output/ -o parquet

# Both formats
abstar run sequences.fasta output/ -o airr -o parquet

Python:

import abstar

# Write to files
abstar.run("sequences.fasta", "output/", output_format=["airr", "parquet"])

# Return as DataFrame (no file output)
df = abstar.run("sequences.fasta", as_dataframe=True)

Output Directory Structure

output/
├── airr/                 # AIRR TSV files
│   └── sequences.tsv
├── parquet/              # Parquet files
│   └── sequences.parquet
└── logs/                 # Log files
    └── abstar.log

Output Fields

Core Identification

Field	Type	Description
sequence_id	String	Unique sequence identifier
sequence_input	String	Original input sequence
sequence_oriented	String	Sequence in V->J orientation
rev_comp	Boolean	True if sequence was reverse-complemented
quality	String	Quality scores (if FASTQ input)
umi	String	Unique molecular identifier (if parsed)
locus	String	Locus (e.g., IGH, IGK, IGL, TRA, TRB)
species	String	Species from germline database
germline_database	String	Name of germline database used

Gene Calls

Field	Type	Description
v_call	String	V gene assignment with allele (e.g., IGHV1-2*02)
d_call	String	D gene assignment
j_call	String	J gene assignment
c_call	String	C gene (isotype) assignment
v_gene	String	V gene without allele (e.g., IGHV1-2)
d_gene	String	D gene without allele
j_gene	String	J gene without allele
c_gene	String	C gene without allele
v_support	Float	V gene assignment E-value
d_support	Float	D gene assignment E-value
j_support	Float	J gene assignment E-value
c_support	Float	C gene assignment E-value

Regions

Field	Type	Description
fwr1, fwr1_aa	String	Framework region 1 (nucleotide, amino acid)
cdr1, cdr1_aa	String	CDR1
fwr2, fwr2_aa	String	Framework region 2
cdr2, cdr2_aa	String	CDR2
fwr3, fwr3_aa	String	Framework region 3
cdr3, cdr3_aa	String	CDR3
fwr4, fwr4_aa	String	Framework region 4
junction, junction_aa	String	Junction region (conserved C to conserved W/F)
cdr3_length	Integer	CDR3 length in amino acids
np1, np2	String	N-nucleotide regions (non-templated)
np1_length, np2_length	Integer	Length of N-regions

Junction Components

Field	Type	Description
cdr3_v, cdr3_v_aa	String	V gene contribution to CDR3
cdr3_n1, cdr3_n1_aa	String	N1 region (V-D junction)
cdr3_d, cdr3_d_aa	String	D gene contribution to CDR3
cdr3_n2, cdr3_n2_aa	String	N2 region (D-J junction)
cdr3_j, cdr3_j_aa	String	J gene contribution to CDR3

Quality Metrics

Field	Type	Description
productive	Boolean	True if sequence is productive
productivity_issues	String	List of productivity issues (if any)
stop_codon	Boolean	True if stop codon present
complete_vdj	Boolean	True if V, D (heavy only), and J assigned
v_identity	Float	V gene identity (0-1)
v_identity_aa	Float	V gene amino acid identity
j_identity	Float	J gene identity
frame	Integer	Reading frame (0, 1, or 2)

Mutations

Field	Type	Description
v_mutations	String	V gene mutations (format: “pos:ref>alt”)
v_mutations_aa	String	V gene amino acid mutations
v_mutation_count	Integer	Number of V gene mutations
v_mutation_count_aa	Integer	Number of V gene AA mutations
v_insertions	String	Non-templated insertions in V
v_deletions	String	Non-templated deletions in V
v_frameshift	Boolean	True if frameshift in V region
c_mutations	String	C gene mutations
c_mutation_count	Integer	Number of C gene mutations

Sequences

Field	Type	Description
sequence	String	V(D)J sequence (no leader, no constant)
germline	String	Corresponding germline sequence
sequence_aa	String	Amino acid sequence
germline_aa	String	Germline amino acid sequence
sequence_gapped	String	IMGT-gapped sequence
germline_gapped	String	IMGT-gapped germline
sequence_alignment	String	Aligned sequence (with gaps from alignment)
germline_alignment	String	Aligned germline

Masks

Field	Type	Description
cdr_mask	String	CDR region mask (0=FWR, 1=CDR1, 2=CDR2, 3=CDR3)
gene_segment_mask	String	Gene segment mask (V, D, J, C)
nongermline_mask	String	Mutation position mask

Position Coordinates

Field	Type	Description
v_sequence_start	Integer	V region start in input sequence
v_sequence_end	Integer	V region end in input sequence
v_germline_start	Integer	Start position in V germline
v_germline_end	Integer	End position in V germline
j_sequence_start	Integer	J region start in input sequence
j_sequence_end	Integer	J region end in input sequence