A grammar for describing microbial genotypes and phenotypes
Project description
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.
A JavaScript (Node) version of the package is available on NPM as gnomic-grammar.
Installation
pip install gnomic
Example usage
In this example, we parse “EcGeneA ΔsiteA::promoterB:EcGeneB ΔgeneC” and “ΔgeneA” in gnomic syntax:
>>> from gnomic import *
>>> g1 = Genotype.parse('+Ec/geneA siteA>P.promoterB:Ec/geneB -geneC')
>>> g1.added_features
(Feature(organism=Organism('Escherichia coli'), name='geneB'),
Feature(organism=Organism('Escherichia coli'), name='geneA'),
Feature(type=Type('promoter'), name='promoterB'))
>>> g1.removed_features
(Feature(name='geneC'),
Feature(name='siteA'))
>>> g1.raw
(Mutation(new=FeatureTree(Feature(organism=Organism('Escherichia coli'), name='geneA'))),
Mutation(old=FeatureTree(Feature(name='siteA')),
new=FeatureTree(Fusion(Feature(type=Type('promoter'), name='promoterB'),
Feature(organism=Organism('Escherichia coli'), name='geneB')))),
Mutation(old=FeatureTree(Feature(name='geneC'))))
>>>
>>> g2 = Genotype.parse('-geneA', parent=g1)
>>> g2.added_features
(Feature(type=Type('promoter'), name='promoterB'),
Feature(name='geneB', organism=Organism('Escherichia coli')))
>>> g2.removed_features
(Feature(name='siteA'),
Feature(name='geneC'),
Feature(name='geneA'))
>>> g2.changes()
{Mutation(old=FeatureTree(Feature(name='siteA'))),
Mutation(new=FeatureTree(Feature(name='promoterB', type=Type('promoter')))),
Mutation(new=FeatureTree(Feature(organism=Organism('Escherichia coli'), name='geneB'))),
Mutation(old=FeatureTree(Feature(name='geneC'))),
Mutation(old=FeatureTree(Feature(name='geneA')))}
>>> g2.changes(fusions=True)
{Mutation(old=FeatureTree(Feature(name='siteA'))),
Mutation(new=FeatureTree(Fusion(Feature(name='promoterB', type=Type('promoter')),
Feature(organism=Organism('Escherichia coli'), name='geneB')))),
Mutation(old=FeatureTree(Feature(name='geneC'))),
Mutation(old=FeatureTree(Feature(name='geneA')))}
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 inserted |
+feature |
site replaced with feature |
site>feature |
site (multiple integration) replaced with feature |
site>>feature |
feature of organism |
organism/feature |
feature with variant |
feature(variant) |
feature with accession number |
feature#GB:123456 |
feature by accession number |
#GB:123456 |
fusion of feature1 and feature2 |
feature1:feature2 |
insertion of two fused features |
+feature1:feature2 |
insertion of a list of features or fusions |
+{..insertables} |
phenotype: wild-type |
phene+ or phene(wild-type) |
phenotype: mutant |
phene- or phene(mutant) |
selection marker: used (wild-type) |
marker+ |
selection marker: available (mutant) |
marker- |
a non-integrated plasmid |
plasmid{} or plasmid{..insertables} |
plasmid with selection marker |
plasmid{..insertables}::marker+ |
integrated plasmid vector with required insertion site |
site>vector{..insertables} |
nucleotide range of a feature |
feature[startBase_endBase] |
coding nucleotide range of a gene |
gene[c.startBase_endBase] |
protein amino-acid range of a gene |
gene[p.startAA_endAA] |
protein amino-acid of a gene |
gene[p.AA] |
Development
To rebuild the gnomic parser using grako, run:
grako genotype.enbf -o gnomic/grammar.py -m Gnomic
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