topeology 0.0.2

[](https://travis-ci.org/hammerlab/topeology) [](https://coveralls.io/github/hammerlab/topeology?branch=master)

# Topeology

Topeology compares neoepitope sequences with epitopes from [IEDB](http://www.iedb.org/).

## Example

From the command line:

```sh
topeology --input epitopes.csv --epitope-lengths 8 9 10 11 > scores.csv
```

In Python:

```python
from topeology import compare
output_dataframe = compare('epitopes.csv')
```

Input looks like:

| sample | epitope
| ------ | -------
| 001 | AAALPGKCGV

Output looks like:

| sample | epitope | iedb_epitope | score
| ------ | ------- | ------------ | -----
| 001 | AAALPGKCGV | EFKEFAAGRR | 2.38

## Installation

You can install topeology using [pip]:

```sh
pip install topeology
```

Currently, topeology use [seq-align] to quickly compare sequences, wrapped in a C extension. It will be
installed if [seq-align] is installed; otherwise, topeology reverts to using another scorer.

To install topeology with this extension:
- Follow [seq-align]'s installation instructions, and then set `SEQ_ALIGN_PATH` to the installation
directory.
- Install topeology via [pip]. If topeology is already installed, run `pip install topeology --upgrade --no-deps --force-reinstall`.

## Methodology

Topeology uses Smith-Waterman alignment to align each neoepitope with each IEDB epitope of the
same length, and returns the resultant epitope-epitope scores. Only position 3 to the penultimate
amino acid are considered.

This software uses the following libraries for Smith-Waterman alignment:

- [seq-align]
- [Complete-Striped-Smith-Waterman-Library](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)

[seq-align]: https://github.com/noporpoise/seq-align
[pip]: https://pip.pypa.io/en/latest/quickstart.html