# Using a custom species

By default, `TCRconvertR` 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:

`TCRconvertR` 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_lookup_from_fastas()`

The `species` parameter should be the species name you’ll use when calling `convert_gene()`.

    library(TCRconvertR)

    # For this example, create a temporary input folder
    fastadir <- file.path(tempdir(), "TCRconvertR_tmp")
    dir.create(fastadir, showWarnings = FALSE)
    file.copy(get_example_path("fasta_dir/test_trav.fa"), fastadir)
    #> [1] TRUE

    # Build lookup tables
    new_lookup_dir <- build_lookup_from_fastas(fastadir, species = "rabbit")
    #> Writing lookup tables to: ~/Library/Application Support/TCRconvertR/rabbit

    # Confirm they exist now
    list.files(new_lookup_dir)
    #> [1] "lookup.csv"               "lookup_from_adaptive.csv"
    #> [3] "lookup_from_tenx.csv"

Details:

`species` will also be the name of the folder storing lookup tables, so these characters are not allowed:

`/ \ : * ? " < > | ~ ` \n \t`