Commandline Tools#

Deprecated since version 1.4: The validate repertoire subcommand is deprecated. Use validate airr instead.

airr-tools#

AIRR Community Standards utility commands.

usage: airr-tools [-h] [--version]  ...
-h, --help#

show this help message and exit

--version#

show program’s version number and exit

airr-tools merge#

Merge AIRR rearrangement files.

usage: airr-tools merge [--version] [-h] -o OUT_FILE [--drop] -a AIRR_FILES
                        [AIRR_FILES ...]
--version#

show program’s version number and exit

-h, --help#

show this help message and exit

-o <out_file>#

Output file name.

--drop#

If specified, drop fields that do not exist in all input files. Otherwise, include all columns in all files and fill missing data with empty strings.

-a <airr_files>#

A list of AIRR rearrangement files.

airr-tools validate#

Validate files for AIRR Standards compliance.

usage: airr-tools validate [--version] [-h]  ...
--version#

show program’s version number and exit

-h, --help#

show this help message and exit

airr-tools validate airr#

Validate AIRR Data Model files.

usage: airr-tools validate airr [--version] [-h] -a AIRR_FILES
                                [AIRR_FILES ...]
--version#

show program’s version number and exit

-h, --help#

show this help message and exit

-a <airr_files>#

A list of AIRR Data Model files.

airr-tools validate rearrangement#

Validate AIRR rearrangement files.

usage: airr-tools validate rearrangement [--version] [-h] -a AIRR_FILES
                                         [AIRR_FILES ...]
--version#

show program’s version number and exit

-h, --help#

show this help message and exit

-a <airr_files>#

A list of AIRR rearrangement files.

airr-tools validate repertoire#

Validate AIRR repertoire metadata files.

usage: airr-tools validate repertoire [--version] [-h] -a AIRR_FILES
                                      [AIRR_FILES ...]
--version#

show program’s version number and exit

-h, --help#

show this help message and exit

-a <airr_files>#

A list of AIRR repertoire metadata files.