Metadata-Version: 1.1
Name: description-extractor
Version: 2.3.4
Summary: HGVS variant description extractor
Home-page: https://github.com/mutalyzer/description-extractor
Author: LUMC, Jonathan K. Vis
Author-email: j.k.vis@lumc.nl
License: MIT License
Description: # HGVS variant description extractor
        
        Unambiguous sequence variant descriptions are important in reporting
        the outcome of clinical diagnostic DNA tests. The standard
        nomenclature of the Human Genome Variation Society (HGVS) describes
        the observed variant sequence relative to a given reference sequence.
        We propose an efficient algorithm for the extraction of
        HGVS descriptions from two sequences with three main requirements in
        mind: minimizing the length of the resulting descriptions, minimizing
        the computation time, and keeping the unambiguous descriptions
        biologically meaningful.
        
        This algorithm is able to compute the HGVS descriptions of complete
        chromosomes or other large DNA strings in a reasonable amount of
        computation time and its resulting descriptions are relatively small.
        Additional applications include updating of gene variant database
        contents and reference sequence liftovers.
        
            >>> from extractor import describe_dna
            >>> print describe_dna('TAACAATGGAAC', 'TAAACAATTGAA')
            [3dup;8G>T;12del]
        
        
        ## Implementation
        
        The core algorithm is implemented in C++ with a Python wrapper providing a
        developer friendly interface.
        
        
        ## Installation
        
        ### Python package
        
        You need [SWIG](http://www.swig.org/) installed. Then:
        
            pip install description-extractor
        
        
        ### C++ library only
        
        Run `make`.
        
        Optionally set the `__debug__` flag to trace the algorithm.
        
        For direct use within a C/C++ environment just
        `#include "extractor.h"` and add `extractor.cc` to your project's
        source files.
        
        
        ## Testing
        
        There are some unit tests for the Python interface. After installing the
        Python package, run them using [pytest](http://pytest.org/):
        
            pip install pytest
            python setup.py develop
            py.test
        
        Alternatively, use [tox](https://tox.readthedocs.org/) to automatically run
        the tests on all supported versions of Python:
        
            pip install tox
            tox
        
Keywords: bioinformatics
Platform: any
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: C++
Classifier: Topic :: Scientific/Engineering
