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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

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), (plasmid ...insertables), plasmid{} or plasmid{...insertables}
plasmid with single selection marker (plasmid ...insertables)::marker+
plasmid with multiple selection markers (plasmid ...insertables)::{markerA+ markerB+}
integrated plasmid vector with required insertion site site>(vector ..insertables)
genomic nucleotide range of a feature feature[g.startBase_endBase]

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 *
>>> 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')))}

Development

To rebuild the gnomic parser using grako, run:

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

Release History

0.4.0

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
gnomic-0.4.0.tar.gz (13.5 kB) Copy SHA256 Checksum SHA256 Source Mar 22, 2017

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