Gnomic
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 gnomicLanguage 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
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