My first time installing and running TCRdist3.
Installation and all dependancies seem succcessful.
When running the package on novel data, I have some confusion about the db file. I get many notifications like this:
/home/Myname/.local/lib/python3.11/site-packages/tcrdist/repertoire.py:500: UserWarning: TRAV29DV5 gene was not recognized in reference db no cdr seq could be inferred f0 = lambda v : self._map_gene_to_reference_seq2(gene = v,
This happens for all of the genes. It seems the db file is not being found properly or accessed properly. i've been running the code as follows
tr = TCRrep( cell_df=My_Data, organism='human', chains=['alpha', 'beta'], db_file='alphabeta_gammadelta_db.tsv'
When this doesn't work, I downloaded the file from the Github repo, and saved it in the project folder, and ran the code like this:
`tr = TCRrep(
cell_df=My_Data,
organism='human',
chains=['alpha', 'beta'],
db_file='/folder/home/j/myname/Project_data/alphabeta_gammadelta_db.tsv''
but get this error
/home/j/myname/.local/lib/python3.11/site-packages/tcrdist/repertoire.py:165: UserWarning: db_file must be 'alphabeta_gammadelta_db.tsv' or 'alphabeta_db.tsv' or 'gammadelta_db.tsv' unless you have built tcrdist3 from scratch self._validate_db_file()
I've also tried reading in as a TSV but I cannot get the package to link my sequences to the DB....
Please advise if you can help!
