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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.

Variant: shortcut to SequenceVariant

Variant is an API shortcut to instantiating a SequenceVariant object from an HGVS string. It accepts both gene-name-bearing and non-gene-name-bearing HGVS strings.

See [Human Genome Variation Society](http://www.hgvs.org/) for explanation of HGVS strings.

Examples of valid HGVS strings:

NM_198056.2:c.4786T>A
NC_000023.10:g.32841489delT
NP_009225.1:p.Glu1000_Glu1001del
NM_001165963.1(SCN1A):c.384_1662dup

Note: some valid HGVS strings currently cannot be parsed by the hgvs library (as of 6/17/2016). Examples:

NC_000001.11:g.(?_215888426)_(215900905_?)del
NM_000251.2:c.212-?_366+?dup

When an illogical or invalid HGVS string is provided to Variant, this function returns None. (Tune into the “metavariant” logger at INFO level for information.)

Variant will also accept a SequenceVariant object as its argument, returning the same variant (identity).

VariantLVG: Lexical Variant Generation

VariantLVG takes an hgvs.SequenceVariant object or a plain HGVS string and uses the Universal Transcript Archive (UTA) to find as many related transcripts and sequence variants as possible that could be used as “synonyms” of the provided variant.

This class raises CriticalHgvsError upon instantiation if the supplied HGVS string fails to create a valid SequenceVariant object.

Usage example:

hgvs_text = 'NM_198056.2:c.4786T>A'
lex = VariantLVG(hgvs_text)

print(lex.variants)
print(lex.transcripts)
print(lex.gene_name)

Attributes:

hgvs_text: original hgvs string from instantiation
seqvar: original SequenceVariant from instantiation
transcripts: list of strings indicating related transcripts
variants: 2-level dictionary of shape { seqtype: { hgvs_text: seqvar } }

Properties:

gene_name: returns HUGO gene-name if it can be ascertained using UTA. (Lazy-loaded attribute _gene_name.)
hgvs_c: returns flat list of c.DNA hgvs strings from variants
hgvs_g: returns flat list of g.DNA hgvs strings from variants
hgvs_n: returns flat list of n.RNA hgvs strings from variants
hgvs_p: returns flat list of protein hgvs strings from variants
seqvars: returns flat list of SequenceVariant objects from variants

Methods:

to_dict(): returns non-underscored attributes (seqvar, hgvs_text, transcripts, seqvars) as dictionary

VariantComponents: Parsing and “Slang”

VariantComponents allows instantiation in two different ways: using an hgvs.SequenceVariant object and using a set of components as keyword arguments.

Usage starting from a SequenceVariant object:

comp = VariantComponents(seqvar)

Usage starting from individual components:

comp = VariantComponents(seqtype='c', edittype='SUB', pos='322', ref='C', alt='T')

If no seqtype is supplied, VariantComponents tries to infer the sequence type heuristically (e.g. the presence of a “U” in the ref or the alt implies this is an RNA string).

VariantComponents may raise a RejectedSeqVar exception during instantiation (see “Exceptions” below).

A VariantComponents object provides access to the following attributes and properties:

seqtype: the sequence type of this seqvar (one of 'c', 'g', 'g', 'n')
edittype: the type of mutation represented by this variant ('SUB', 'DEL', 'FS', etc)
pos: position of the edit
ref: reference sequence at given position
alt: alternate (or "wildtype") at given position

posedit: returns the HGVS "official" construction of this seqvar's position + edit information.
posedit_slang: returns a list of algorithmically generated "slang" for given seqvar's posedit.

Exceptions

All exceptions can be found and imported from metavariant.exceptions.

CriticalHgvsError: raised when input HGVS string fails to instantiate a SequenceVariant object within the VariantLVG object.

RejectedSeqVar: raised inside VariantComponents when input sequence components fail certain tests of completeness. For example, a protein seqvar will throw this Exception if the protein effect string is only a “?” (i.e. unknown protein effect). A “SUB” (substitution) will fail the completeness test if an “alt” is not provided in the instantiated components.

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

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