gnomic 1.0.1

A grammar for describing microbial genotypes and phenotypes

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

• Wikipedia — Bacterial genetic nomenclature

• Journal of Bacteriology — Instructions to Authors

• Human Genome Variation Society — Recommendations for the description of sequence variants

• Databases cross-referenced in UniProtKB