https://github.com/hammerlab/topeology
Compare neoepitope sequences with epitopes from IEDB
https://github.com/hammerlab/topeology
Last synced: 3 months ago
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Compare neoepitope sequences with epitopes from IEDB
- Host: GitHub
- URL: https://github.com/hammerlab/topeology
- Owner: hammerlab
- Created: 2015-09-05T22:01:02.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-12-12T15:07:48.000Z (over 7 years ago)
- Last Synced: 2025-09-10T09:31:43.914Z (9 months ago)
- Language: Python
- Homepage:
- Size: 59.6 KB
- Stars: 3
- Watchers: 11
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
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README
[](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/).
Note: Topeology is no longer being actively maintained.
## 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]:
```sh
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
directory.
- 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](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)
[seq-align]: https://github.com/noporpoise/seq-align
[pip]: https://pip.pypa.io/en/latest/quickstart.html