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A grammar for describing microbial genotypes and phenotypes

Project description

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Gnomic is a human– and computer–readable representation of microbial genotypes and phenotypes. The gnomic Python package contains a parser for the Gnomic grammar able to interpret changes over multiple generations.

The first formal guidelines for microbial genetic nomenclature were drawn up in the 1960s. These traditional nomenclatures are too ambiguous to be useful for modern computer-assisted genome engineering. The gnomic grammar is an improvement over existing nomenclatures, designed to be clear, unambiguous, computer–readable and describe genotypes at various levels of detail.

Installation

pip install gnomic

Language grammar

The grammar consists of a list of genotype or phenotype designations, separated by spaces and/or commas. The designations are described using the following nomenclature:

Designation

Grammar expression

feature deleted

-feature

feature at locus deleted

-feature@locus

feature inserted

+feature

site replaced with feature

site>feature

site (multiple integration) replaced with feature

site>>feature

site at locus replaced with feature

site@locus>feature

feature of organism

organism/feature

feature with type

type.feature

feature with variant

feature(variant)

feature with list of variants

feature(var1, var2) or feature(var1; var2)

feature with accession number

feature#GB:123456

feature by accession number

#GB:123456

accession number

#database:id or #id

fusion of feature1 and feature2

feature1:feature2

insertion of two fused features

+feature1:feature2

insertion of a list of features or fusions

+{..insertables}

fusion of a list and a feature

{..insertables}:feature

a non-integrated plasmid

(plasmid) or (plasmid ...insertables)

integrated plasmid vector with required insertion site

site>(vector ..insertables)

Feature variants

Features may have one or more variants, separated by colon “;” or comma “,”.

For example: geneX(cold-resistant; heat-resistant)

Variants can either be identifiers (using the characters a-z, 0-9, “-” and “_”) or be sequence variants following the HGVS Sequence Variant Nomenclature.

For example: geneY(c.123G>T)

Example usage

In this example, we parse “EcGeneA ΔsiteA::promoterB:EcGeneB ΔgeneC” and “ΔgeneA” in gnomic syntax:

>>> from gnomic import Genotype
>>> g1 = Genotype.parse('+Ec/geneA(variant) siteA>P.promoterB:Ec/geneB -geneC')
>>> g1.added_features
{Feature(organism='Ec', name='geneA', variant=('variant',)),
 Feature(organism='Ec', name='geneB'),
 Feature(type='P', name='promoterB')}
>>> g1.removed_features
{Feature(name='geneC'),
 Feature(name='siteA')}

>>> g2 = Genotype.parse('-geneA', parent=g1)
>>> g2.added_features
{Feature(type='P', name='promoterB'),
 Feature(name='geneB', organism='Ec')}
>>> g2.removed_features
{Feature(name='siteA'),
 Feature(name='geneC')}
 >>> g2.changes()
 (Change(multiple=False,
         after=Fusion(annotations=(Feature(type='P', name='promoterB'), Feature(organism='Ec', name='geneB'))),
         before=Feature(name='siteA')),
  Change(multiple=False, before=Feature(name='geneC')))

 >>> g2.format()
 'ΔsiteA→P.promoterB:Ec/geneB ΔgeneC'

Development

To rebuild the gnomic parser using grako (version 3.18.1), run:

grako gnomic-grammar/genotype.enbf -o gnomic/grammar.py -m Gnomic

References

Project details


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