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Compare epitope homology

Project Description

[![Build Status](https://travis-ci.org/hammerlab/topeology.svg?branch=master)](https://travis-ci.org/hammerlab/topeology) [![Coverage Status](https://coveralls.io/repos/hammerlab/topeology/badge.svg?branch=master&service=github)](https://coveralls.io/github/hammerlab/topeology?branch=master)

# Topeology

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

This software is not currently ready for production use.

## 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](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. Only position 3 to the penultimate amino acid are considered.

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

Release History

Release History

This version
History Node

0.0.3

History Node

0.0.2

History Node

0.0.1

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topeology-0.0.3.tar.gz (9.0 kB) Copy SHA256 Checksum SHA256 Source Jan 29, 2016

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