mhctools
mhctools is a Python library for running MHC binding, presentation, immunogenicity, and antigen-processing predictors. It provides a common interface to tools such as NetMHCpan and MHCflurry, with results you can inspect in Python or export as a pandas DataFrame.
Read the getting started guide or browse the documentation.
Install and predict
Requires Python 3.11 or later and pandas 3.x.
pip install mhctools
mhctools fetch mhcflurry
from mhctools import MHCflurry
predictor = MHCflurry(alleles=["HLA-A*02:01", "HLA-B*07:02"])
results = predictor.predict(["SIINFEKL", "GILGFVFTL"])
for result in results:
affinity = result.affinity
if affinity is not None:
print(result.peptide, affinity.allele, affinity.value)
Each result corresponds to one input peptide. The affinity accessor selects
the strongest prediction across alleles, with IC50 in nM. Use
predict_dataframe() for a pandas table or predict_proteins() to scan protein
sequences. See results and DataFrames.
Most predictors need model weights or an external installation. Use
mhctools ls to locate models and mhctools predictors to check which can run.
The installation guide explains
downloads, optional backends, and licensing.
Command line
Run mhctools --help to see commands and prediction options, or
mhctools --version to identify the installed release.
Enable Bash/zsh tab completion for this shell:
eval "$(register-python-argcomplete mhctools)"
Alternatively, run activate-global-python-argcomplete once and start a new
shell to enable completion for all participating OpenVax tools. See the
command-line guide for details.
Guides
- Choosing a predictor and known limits
- Predictor matrix: Python classes, CLI names, inputs, and installation routes
- Recipes: protein scans, multiple samples, and table annotation
- Command line
- Peptidase activity, vaccine reports, and benchmarks
Development
./develop.sh
./lint.sh
./test.sh
See the testing guide and release instructions.
5 maintainers
Metadata
5 maintainers
Release files for mhctools 4.8.1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| mhctools-4.8.1.tar.gz | 1.2 MB | Without provenance | Details for mhctools-4.8.1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| mhctools-4.8.1-py3-none-any.whl | Python 3 | none | any | Details for mhctools-4.8.1-py3-none-any.whl |
Total release size: 2.1 MB
Release files / mhctools-4.8.1.tar.gz
| Download URL | mhctools-4.8.1.tar.gz |
|---|---|
| Size | 1.2 MB |
| Tags | Source |
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Release files / mhctools-4.8.1-py3-none-any.whl
| Download URL | mhctools-4.8.1-py3-none-any.whl |
|---|---|
| Size | 902.8 kB |
| Tags | Python 3 |
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