Compare epitope homology
Project description
[](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.
](https://travis-ci.org/hammerlab/topeology){kind=link}
](https://coveralls.io/github/hammerlab/topeology){kind=link}