Library: 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_lookup_from_fastas()

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

import tcrconvert
import os

# Using our example directory of fasta files
fastadir = tcrconvert.get_example_path('fasta_dir')

# Build lookup tables and note where they're being written to
new_lookup_dir = tcrconvert.build_lookup_from_fastas(fastadir, species='rabbit')
new_lookup_dir

'/home/docs/.local/share/tcrconvert/rabbit'

Confirm they exist there:

os.listdir(new_lookup_dir)

['lookup.csv', 'lookup_from_adaptive.csv', '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