help:¶

--version

show program's version number and exit

-h, --help

show this help message and exit

subcommands:¶

Database operation

airr

Converts input to an AIRR TSV file.

changeo

Converts input into a Change-O TSV file.

fasta

Creates a fasta file from database records.

baseline

Creates a specially formatted fasta file from database records for input into the BASELINe website. The format groups clonally related sequences sequentially, with the germline sequence preceding each clone and denoted by headers starting with ">>".

genbank

Creates files for GenBank/TLS submissions.

output files:¶

airr

AIRR formatted database files.

changeo

Change-O formatted database files.

sequences

FASTA formatted sequences output from the subcommands fasta and clip.

genbank

feature tables and fasta files containing MiAIRR compliant input for tbl2asn.

required fields:¶

sequence_id, sequence, sequence_alignment, junction, v_call, d_call, j_call, v_germline_start, v_germline_end, v_sequence_start, v_sequence_end, d_sequence_start, d_sequence_end, j_sequence_start, j_sequence_end

optional fields:¶

germline_alignment, c_call, clone_id