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Compare epitope homology

Project description

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# Topeology

Topeology compares neoepitope sequences with epitopes from [IEDB](

## 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
—— | ——- | ———— | —–

## Installation

You can install topeology using [pip](

`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.

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