Name: topeology
Owner: Hammer Lab
Description: Compare neoepitope sequences with epitopes from IEDB
Created: 2015-09-05 22:01:02.0
Updated: 2017-02-17 20:30:20.0
Pushed: 2016-12-14 17:34:43.0
Size: 62
Language: Python
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Topeology compares neoepitope sequences with epitopes from IEDB.
From the command line:
ology --input epitopes.csv --epitope-lengths 8 9 10 11 > scores.csv
In Python:
topeology import compare
ut_dataframe = compare('epitopes.csv')
Input looks like:
| sample | epitope | —— | ——- | 001 | AAALPGKCGV
Output looks like:
| sample | epitope | iedb_epitope | score | —— | ——- | ———— | —– | 001 | AAALPGKCGV | EFKEFAAGRR | 2.38
You can install topeology using 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:
SEQ_ALIGN_PATH to the installation
directory.pip install topeology --upgrade --no-deps --force-reinstall.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: