Welcome to Gnomic’s documentation!¶
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 and computer–readable and describe genotypes at various levels of detail.
A JavaScript (Node) version of the package is available on NPM as gnomic-grammar.
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=Organism('Ec'), name='geneA', variant=('variant',)),
Feature(organism=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'