Command-line: Custom Species

By default, TCRconvert supports alpha-beta and gamma-delta V, D, J, and C genes for human, mouse, and rhesus macaque from the IMGT F+ORF+in-frame P references. For other species, follow these steps:

1. Create a folder of IMGT FASTA files

The simplest way is to download from IMGT.

Details:

TCRconvert expects a folder containing files ending in .fasta or .fa with headers in the IMGT format:

>SomeText|TRBV10-1*02|MoreText|...

The sequences are not used, so a text file containing headers and ending in .fa would also work.

2. Run build

The --species/-s flag should be followed by the species name you’ll use when running convert.

Here we’re using our example directory of fasta files as input.

!tcrconvert build \
    --input ../../tcrconvert/examples/fasta_dir \
    --species rabbit

Lookup table written to: /home/docs/.local/share/tcrconvert/rabbit