Usage
Note
As stated on the home page, there is currently limited support for non-human species. Support for more species are planned for the future.
Standardising TCR/MHC gene names
These are tidytcells’ primary usecases.
The API for standardising TCR and MHC genes are similar: tidytcells.tcr.standardise() and tidytcells.mhc.standardise() respectively.
At their core, these functions take as input a potentially non-standard string representation of a gene or allele and returns (if possible) an IMGT-standardised version of the gene/allele name.
In both cases, standardize is a valid alias of the function as well.
Other MHC utilities
tidytcells also provides some extra utilities in the mhc module, including get_chain and get_class.
Example usage
>>> import tidytcells
>>> # --- TCR parsing ---
>>> tidytcells.tcr.standardise('TCRAV32S1', 'homosapiens')
'TRAV25'
>>> tidytcells.tcr.standardise('TRBV1*01', 'homosapiens', enforce_functional=True)
None
>>> tidytcells.tcr.standardise('TRAJ12*01', 'musmusculus', precision='gene')
'TRAJ12'
>>> # --- MHC parsing ---
>>> tidytcells.mhc.standardise('HLA-A', 'homosapiens')
'HLA-A'
>>> tidytcells.mhc.standardise('A1', 'homosapiens')
'HLA-A*01'
>>> tidytcells.mhc.standardise('HLA-B*07:02:01:01', 'homosapiens', precision='protein')
('HLA-B*07:02', ':01:01')
>>> tidytcells.mhc.standardise('HLA-DR1BL')
'HLA-DRB9'
>>> tidytcells.mhc.get_chain('HLA-A')
'alpha'
>>> tidytcells.mhc.get_class('HLA-DRB1*01:01')
2
Supported species and species strings
For all functions that expect a species to be specified via a string, the species should be referred to by its binomial name, lowercased, with no space between the two parts (e.g. 'homosapiens').
That being said, for backwards-compatibility and user friendliness, any combination of camelcasing, uppercasing and the use of whitespace is technically allowed and recognised by the software.
Below is a list of currently supported species:
tidytcells.mhc.get_chain()homosapiens
tidytcells.mhc.get_class()homosapiens
tidytcells.mhc.standardise()homosapiensmusmusculus
tidytcells.tcr.standardise()homosapiensmusmusculus