a lexical manipulation toolkit for genetic variant descriptors (hgvs, etc)
Python toolkit for parsing HGVS strings describing genetic variants (mutations) into components and generating lexical synonyms of these descriptors.
You’ll need a UNIX-like environment to use this package. Both OS X and Linux have been confirmed to work.
Additionally, your system must contain the C development version of the client library for Postgres 9.3 or later (needed to connect to UTA services).
On OS X using brew:
$ brew install postgresql
On Linux using Ubuntu:
$ apt-get install libpq-dev
Python library dependencies for variant_lexicon are the following:
numpy biopython uta hgvs
The above “should” be successfully installed by using setup.py and/or by installing this package via pip.
Optional but Recommended: IPython
Install ipython via pypi:
$ pip install ipython
More installation options and instructions are available on the iPython installation page.
HgvsLVG: Lexical Variant Generation
Let’s say you’ve been handed an HGVS string describing a seen variant. Examples:
NM_ NC_ NP_
HgvsComponents: Parsing and “Slang”
Let’s say you have discovered in clinical literature a some text referring to mutations, described in a few different ways (aka “variant slang”), for example:
410 T>C Arg459Pro
Support and Maintenance
This library was developed in-house at Text2Gene, LLC.
It is provided to the community free of charge by way of the Apache 2.0 License.
You are free to modify it for commercial and non-commercial uses; just don’t try to sell it as-is.
Contributions, extensions, bug reports, suggestions, and swear words all happily accepted, in that order.
email@example.com 2016 and onwards
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