topeology 0.0.0

[](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

Given a CSV file that contains the following columns: sample, epitope, usage is as follows.

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') `

Output looks like:

## Installation

You can install topeology using [pip](https://pip.pypa.io/en/latest/quickstart.html):

`sh pip install topeology `

## 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.