Skip to main content

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/).

## 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:

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.

Project details


Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page