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Compare epitope homology

Project description

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# Topeology

Topeology compares neoepitope sequences with epitopes from [IEDB](

## Example

From the command line:

topeology --input epitopes.csv --epitope-lengths 8 9 10 11 > scores.csv

In Python:

from topeology import compare
output_dataframe = compare('epitopes.csv')

Input looks like:

| sample | epitope
| ------ | -------

Output looks like:

| sample | epitope | iedb_epitope | score
| ------ | ------- | ------------ | -----

## Installation

You can install topeology using [pip]:

pip install topeology

Currently, topeology use [seq-align] to quickly compare sequences, wrapped in a C extension. It will be
installed if [seq-align] is installed; otherwise, topeology reverts to using another scorer.

To install topeology with this extension:
- Follow [seq-align]'s installation instructions, and then set `SEQ_ALIGN_PATH` to the installation
- Install topeology via [pip]. If topeology is already installed, run `pip install topeology --upgrade --no-deps --force-reinstall`.

## 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:

- [seq-align]
- [Complete-Striped-Smith-Waterman-Library](


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