tidytcells 0.0.2

Standardise TCR/MHC gene names to IMGT nomenclature.

tidytcells

DISCLAIMER: This package currently only supports parsing of human TCR and MHC gene data. Support for more species is planned for the future.

tidytcells is a lightweight Python package written for bioinformaticians who work with T cell receptor (TCR) data. The main purpose of the package is to solve the problem of parsing and collating together non-standardised TCR datasets. It is often difficult to compile TCR data from multiple sources because the formats/nomenclature of how each dataset encodes TCR and MHC gene names are slightly different, or even inconsistent within themselves. tidytcells attempts to ameliorate this issue by providing simple functions that can, among other things, standardise TCR and MHC gene names to be IMGT-compliant.

The package is currently in its alpha stage in development. More thorough documentation will follow soon.

Table of contents

1. Installation
2. API reference
   • mhc submodule
   • tcr submodule
3. Example usage
4. Contributions

Installation

Installation method	Comments
PyPI (recommended)	pip install tidytcells
source	Download the source code and run pip install . from the project root directory

API reference

tidytcells currently comes with two submodules that can directly be accessed from the parent module: tidytcells.mhc and tidytcells.tcr.

.mhc submodule

.standardise(gene_name: str, species: str)

Attempt to standardise gene_name for species to be IMGT-compliant.

Parameters	Type	Value
gene_name	str	Potentially non-standard name for MHC gene
species	str	Species to which the MHC gene belongs (see below)

Return type

Value

Tuple[Union[str, None], Union[str, None]]

If the specified species is supported, and gene_name could be standardised, then return a tuple containing the standardised gene name decomposed into two parts: 1) the name of the gene specific to the level of the protein, and 2) (if any) further valid specifier fields. If species is unsupported, then return a tuple with the gene_name as is for the first element, and None for the second element. Else return the tuple (None, None). See example usage.

.get_chain(gene_name: str)

NOTE: This function currently only supports HLA gene names.

Given an IMGT-compliant MHC gene name gene_name, detect whether it codes for an alpha chain or a beta chain.

Parameters	Type	Value
gene_name	str	IMGT-compliant MHC gene name

Return type	Value
Union[str, None]	'alpha' or 'beta' if gene_name recognised, else None

.classify(gene_name: str)

NOTE: This function currently only supports HLA gene names.

Given an IMGT-compliant MHC gene name gene_name, detect whether it comprises a class I or II MHC receptor.

Parameters	Type	Value
gene_name	str	IMGT-compliant MHC gene name

Return type	Value
Union[int, None]	1 or 2 if gene_name recognised, else None

.tcr submodule

.standardise(gene_name: str, species: str)

Attempt to standardise gene_name for species to be IMGT-compliant.

Parameters	Type	Value
gene_name	str	Potentially non-standard name for TCR gene
species	str	Species to which the TCR gene belongs (see below)

Return type	Value
Union[str, None]	If the specified species is supported, and gene_name could be standardised, then return the standardised gene name. If species is unsupported, then return gene_name as is. Else return None.

Species names

For all functions that expect a species to be specified via a string, the species should be referred to by its binomial name (genus followed by species), CamelCased, with no space between the two parts (e.g. 'HomoSapiens').

Example usage

import tidytcells


# --- MHC parsing ---


tidytcells.mhc.standardise('HLA-A', 'HomoSapiens')
# > ('HLA-A', None)

tidytcells.mhc.standardise('B07', 'HomoSapiens')
# > ('HLA-B*07', None)

tidytcells.mhc.standardise('DRA*01:01:01', 'HomoSapiens')
# > ('HLA-DRA*01:01', ':01')

tidycells.mhc.get_chain('HLA-A')
# > 'alpha'

tidycells.mhc.classify('HLA-DRB1*01:01')
# > 2


# --- TCR parsing ---


tidycells.tcr.standardise('TCRAV32S1', 'HomoSapiens')
# > 'TRAV25'

Contributions

Please feel free to contribute by submitting bug reports and pull requests.