Metadata-Version: 1.1
Name: topeology
Version: 0.0.2
Summary: Compare epitope homology
Home-page: https://github.com/hammerlab/topeology
Author: Tavi Nathanson
Author-email: tavi {dot} nathanson {at} gmail {dot} com
License: http://www.apache.org/licenses/LICENSE-2.0.html
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
        
        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
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
