Documentation

DocumentationAPI Reference

// api reference

API Reference

Complete reference for AlignAIR command-line interface, parameters, input formats, and output schemas.

// jump to

CLI Interface Parameters Input Formats Output Schema

// 01 / cli

Command Line Interface

basic syntax

python app.py [COMMAND] [OPTIONS]

available commands

run

Execute AlignAIR sequence analysis with specified parameters.

primary

--help

Display help information and parameter list.

utility

--version

Show AlignAIR version information.

utility

exit codes

0Success

1General error

2Invalid arguments

3File not found

// 02 / parameters

Complete parameters reference

required

Parameter	Type	Description	Example
`--model-checkpoint`	string	Path to trained model weights	`/app/pretrained_models/IGH_S5F_576`
`--chain-type`	choice	heavy \| light	`heavy`
`--sequences`	string	Path to input sequence file	`/data/input/sequences.csv`
`--save-path`	string	Output directory path	`/data/output`

model configuration

--max-input-size

int (default: 576)

Maximum sequence length

--batch-size

int (default: 2048)

Processing batch size

threshold settings

--v-allele-threshold

float (default: 0.75)

V gene threshold

--d-allele-threshold

float (default: 0.3)

D gene threshold

--j-allele-threshold

float (default: 0.8)

J gene threshold

--v-cap / --d-cap / --j-cap

int (default: 3)

Maximum calls per gene

processing options

--airr-format

flag

Output full AIRR schema

--fix-orientation

flag

Auto-correct sequence orientation

--translate-to-asc

flag

Use ASC allele names

--save-predict-object

flag

Save raw predictions for debugging

// 03 / input formats

Input formats

CSV

Required column: sequence

sequence_id,sequence
seq_001,CAGGTGCAGCTG…
seq_002,GAGGTGCAGCTG…

TSV

Tab-separated values

sequence_id	sequence
seq_001	CAGGTGCAGCTG…
seq_002	GAGGTGCAGCTG…

FASTA

Standard >header format

>seq_001
CAGGTGCAGCTGGTGGAG…
>seq_002
GAGGTGCAGCTGGTGGAG…

// valid sequences

DNA nucleotides: A, T, G, C
IUPAC ambiguous codes: N, R, Y, etc.
Minimum length: 50 nucleotides
Maximum length: auto-trimmed to max-input-size

// invalid sequences

Protein sequences (amino acids)
Empty or whitespace-only sequences
Sequences with invalid characters
Extremely short sequences (< 50 nt)

// 04 / output schema

Output schema

standard columns

Column	Type	Description	Example
`sequence_id`	string	Unique sequence identifier	`seq_001`
`v_call`	string	V gene assignment(s)	`IGHV1-2*01`
`d_call`	string	D gene assignment(s)	`IGHD3-3*01`
`j_call`	string	J gene assignment(s)	`IGHJ4*01`
`productive`	boolean	Sequence productivity status	`True`
`sequence`	string	Input sequence (preserved)	`CAGGTG…`