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 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:

pip install pytest
python setup.py develop
py.test

Alternatively, use tox to automatically run the tests on all supported versions of Python:

pip install tox
tox