Installation

autoDCR runs on Python3. As of version 0.3.0, it’s made using poetry and typer. It can be installed from PyPI:

pip install autoDCR

(Note that the last non-package version (0.2.7) is available as a release from the Github repo, which is the version used in the 2022 stitchr paper.)

In order to download the necessary TCR germline reference data, IMGTgeneDL is also required. If it’s not automatically installed alongside stitchr, it can be installed with:

pip install IMGTgeneDL

General usage

  • AutoDCR is run in the command line using a number of different subcommands, e.g. autoDCR subcommand -x -y -z parameters.

  • The --help / -h flag can be used to list either:

    • The different subcommands available (autoDCR -h)…

    • … Or the parameters associated with a subcommand (autoDCR subcommand -h).

  • This help page gives details as to the types and default values for the different editable parameters.