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a lexical manipulation toolkit for genetic variant descriptors (hgvs, etc)

Project description

Python toolkit for parsing HGVS strings describing genetic variants (mutations) into components and generating lexical synonyms of these descriptors.

Requirements

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.

HgvsLVG: Lexical Variant Generation

(Discussion)

Let’s say you’ve been handed an HGVS string describing a seen variant. Examples:

NM_
NC_
NP_

VariantLVG

HgvsComponents: Parsing and “Slang”

(Discussion)

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

VariantComponents

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.

naomi@nthmost.com 2016 and onwards

Project details


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