{ "info": { "author": "brentp", "author_email": "bpederse@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Text Processing" ], "description": "------------------------------------------------------------------------------\nnwalign: fast `cython`_ - `Needleman-Wunsch`_ alignment\n------------------------------------------------------------------------------\n\n.. _`Needleman-Wunsch`: http://en.wikipedia.org/wiki/Needleman-Wunsch_algorithm \n.. _`scoring matrix`: http://en.wikipedia.org/wiki/Substitution_matrix\n.. _`cython`: http://cython.org\n\nThis module provides a python module and a command-line interface to do global-\nsequence alignment using the `Needleman-Wunsch` algorithm. It uses `cython`_ \nand numpy for speed.\n\nCommand-Line Usage \n==================\nthe nwalign executable is installed to the PATH by setuptools\n::\n\n $ nwalign alphabet alpet\n alphabet\n alp---et\n\nspecify an alignment `scoring matrix`_ \n::\n\n $ nwalign --matrix /usr/share/ncbi/data/BLOSUM62 EEAEE EEEEG\n EEAEE-\n EE-EEG\n\nwith specified penalties\n::\n\n $ nwalign --gap_open -10 --gap_extend -4 --match 12 ASDFF ASFF\n ASDFF\n AS-FF\n\n\nPython Usage\n============\nAlignment\n---------\n::\n\n >>> import nwalign as nw\n >>> nw.global_align(\"CEELECANTH\", \"PELICAN\", matrix='PAM250')\n ('CEELE-CANTH', '-PEL-ICAN--')\n\n # with a specified penalty for open and extend.\n >>> nw.global_align(\"CEELECANTH\", \"PELICAN\", gap_open=-10, gap_extend=-4, matrix='PAM250')\n ('CEELECANTH', '-PELICAN--')\n\n\nthe `matrix` is specified as the full path to an `scoring matrix`_ as\nis distributed with the NCBI toolset.\n\nScoring\n-------\nget the score of an alignment. 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