Metadata-Version: 2.1
Name: mhctools
Version: 1.9.0
Summary: Python interface to running command-line and web-based MHC binding predictors
Home-page: https://github.com/openvax/mhctools
Author: Alex Rubinsteyn, Julia Kodysh, Tim O'Donnell
Author-email: alex@openvax.org, julia@openvax.org, tim@openvax.org
License: http://www.apache.org/licenses/LICENSE-2.0.html
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.7
Requires-Dist: pandas>=0.13.1
Requires-Dist: varcode>=0.5.9
Requires-Dist: pyensembl>=1.0.3
Requires-Dist: sercol>=0.0.2
Requires-Dist: mhcflurry>=2.0.0
Requires-Dist: mhcnames>=0.3.2

[![Build Status](https://travis-ci.org/openvax/mhctools.svg?branch=master)](https://travis-ci.org/openvax/mhctools) [![Coverage Status](https://coveralls.io/repos/openvax/mhctools/badge.svg?branch=master)](https://coveralls.io/r/openvax/mhctools?branch=master)
<a href="https://pypi.python.org/pypi/mhctools/">
    <img src="https://img.shields.io/pypi/v/mhctools.svg?maxAge=1000" alt="PyPI" />
</a>
<!-- 
<a href='https://mhctools.readthedocs.io/en/latest/?badge=latest'>
    <img src='https://readthedocs.org/projects/mhctools/badge/?version=latest' alt='Documentation Status' />
</a>
--> 
<!-- 
[![DOI](https://zenodo.org/badge/18834/openvax/mhctools.svg)](https://zenodo.org/badge/latestdoi/18834/openvax/mhctools)
-->

# mhctools
Python interface to running command-line and web-based MHC binding predictors.

## Commandline examples

### Prediction for user-supplied peptide sequences
```sh
mhctools --sequence SIINFEKL SIINFEKLQ --mhc-predictor netmhc --mhc-alleles A0201
```

### Automatically extract peptides as subsequences of specified length
```sh
mhctools --sequence AAAQQQSIINFEKL --extract-subsequences --mhc-peptide-lengths 8-10 --mhc-predictor mhcflurry --mhc-alleles A0201
```

## Python usage

```python
from mhctools import NetMHCpan
# Run NetMHCpan for alleles HLA-A*01:01 and HLA-A*02:01
predictor = NetMHCpan(alleles=["A*02:01", "hla-a0101"])

# scan the short proteins 1L2Y and 1L3Y for epitopes
protein_sequences = {
  "1L2Y": "NLYIQWLKDGGPSSGRPPPS",
  "1L3Y": "ECDTINCERYNGQVCGGPGRGLCFCGKCRCHPGFEGSACQA"
}

binding_predictions = predictor.predict_subsequences(protein_sequences, peptide_lengths=[9])

# flatten binding predictions into a Pandas DataFrame
df = binding_predictions.to_dataframe()

# epitope collection is sorted by percentile rank
# of binding predictions
for binding_prediction in binding_predictions:
    if binding_prediction.affinity < 100:
        print("Strong binder: %s" % (binding_prediction,))
```

## API

The following MHC binding predictors are available in `mhctools`:
* `MHCflurry`: open source predictor installed by default with `mhctools`, requires the user run `mhcflurry-downloads fetch` first to download MHCflurry models
* `NetMHC3`: requires locally installed version of [NetMHC 3.x](http://www.cbs.dtu.dk/services/NetMHC-3.4/)
* `NetMHC4`: requires locally installed version of [NetMHC 4.x](http://www.cbs.dtu.dk/services/NetMHC/)
* `NetMHC`: a wrapper function to automatically use `NetMHC3` or `NetMHC4` depending on what's installed.
* `NetMHCpan`: requires locally installed version of [NetMHCpan](http://www.cbs.dtu.dk/services/NetMHCpan/)
* `NetMHCIIpan`: requires locally installed version of [NetMHCIIpan](http://www.cbs.dtu.dk/services/NetMHCIIpan/)
* `NetMHCcons`: requires locally installed version of [NetMHCcons](http://www.cbs.dtu.dk/services/NetMHCcons/)
* `IedbMhcClass1`: Uses IEDB's REST API for class I binding predictions.
* `IedbMhcClass2`: Uses IEDB's REST API for class II binding predictions.
* `RandomBindingPredictor`: Creates binding predictions with random IC50 and percentile rank values.

Every binding predictor is constructed with an `alleles` argument specifying the HLA type for which to make predictions. Predictions are generated by calling the `predict` method with a dictionary mapping sequence IDs or names to amino acid sequences.

Additionally there is a module for running the [NetChop](http://www.cbs.dtu.dk/services/NetChop)  proteosomal cleavage predictor:
* `NetChop`: requires locally installed version of [NetChop-3.1](http://www.cbs.dtu.dk/services/NetChop/)
