parasail 1.0.0

pairwise sequence alignment library

# parasail-python: Python Bindings for the Parasail C Library

Author: Jeff Daily ([e-mail])

## Table of Contents

• [Installation](#installation)

• [Citing parasail](#citing-parasail)

• [License: Battelle BSD-style](#license-battelle-bsd-style)

This package contains Python bindings for [parasail](https://github.com/jeffdaily/parasail). Parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.

## Installation

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Once you have installed parasail into –prefix=$PREFIX, you can also compile the Python bindings. Don’t forget to add $PREFIX/lib to your LD_LIBRARY_PATH, if needed. The Python bindings are in the <parasail>/bindings/python directory. To build, run:

` PARASAIL_PREFIX=$PREFIX python setup.py build `

This will correctly setup the necessary CPPFLAGS, LDFLAGS, and LIBS variables during the build. Because the parasail.h header uses C99 keywords, e.g., restrict, the setup.py process will test your C compiler for the correct use of restrict, automatically.

The Python interface only includes bindings for the dispatching functions, not the low-level instruction set-specific function calls. The Python interface also includes wrappers for the various PAM and BLOSUM matrices included in the distribution.

Example:

`python import parasail result = parasail.sw_scan_16("asdf", "asdf", -11, -1, parasail.blosum62) result = parasail.sw_stats_striped_8("asdf", "asdf", -11, -1, parasail.pam100) `

## Citing parasail

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If needed, please cite the following paper.

Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z

http://dx.doi.org/10.1186/s12859-016-0930-z

## License: Battelle BSD-style

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Copyright (c) 2015, Battelle Memorial Institute

1. Battelle Memorial Institute (hereinafter Battelle) hereby grants permission to any person or entity lawfully obtaining a copy of this software and associated documentation files (hereinafter “the Software”) to redistribute and use the Software in source and binary forms, with or without modification. Such person or entity may use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and may permit others to do so, subject to the following conditions:

   • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers.

   • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

   • Other than as used herein, neither the name Battelle Memorial Institute or Battelle may be used in any form whatsoever without the express written consent of Battelle.

   • Redistributions of the software in any form, and publications based on work performed using the software should include the following citation as a reference:

   Daily, Jeff. (2016). Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments. BMC Bioinformatics, 17(1), 1-11. doi:10.1186/s12859-016-0930-z

2. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL BATTELLE OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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