D. discoideum Mutant Phenotypes (dicty.phenotypes)

This modules provides an interface to Dictyostelium mutant phenotypes data from the dictyBase. The mutants are presented as DictyMutant objects with their respective name, strain descriptor, associated genes and associated phenotypes.

>>> from orangecontrib.bio.dicty.phenotypes import *
>>> # Create a set of all mutant objects
>>> dicty_mutants = mutants()
>>> # List a set of all genes referenced by a single mutant
>>> print(mutant_genes(dicty_mutants[0]))
  ['acbA']
>>> # List a set of all phenotypes referenced by a single mutant
>>> print(mutant_phenotypes(dicty_mutants[0]))
  ['decreased lipid binding']

Classes and Functions

Mutant Phenotypes

orangecontrib.bioinformatics.dicty.phenotypes.mutants()[source]

Return all DictyMutant objects.

orangecontrib.bioinformatics.dicty.phenotypes.genes()[source]

Return a set of all genes referenced in the Dictybase.

orangecontrib.bioinformatics.dicty.phenotypes.phenotypes()[source]

Return a set of all phenotypes referenced in Dictybase.

orangecontrib.bioinformatics.dicty.phenotypes.mutant_genes(mutant)[source]

Return a set of all genes referenced by a mutant in Dictybase.

orangecontrib.bioinformatics.dicty.phenotypes.mutant_phenotypes(mutant)[source]

Return a set of all phenotypes referenced by a mutant in Dictybase.

orangecontrib.bioinformatics.dicty.phenotypes.gene_mutants()[source]

Return a dictionary { gene: set(mutant_objects for mutant), … }.

orangecontrib.bioinformatics.dicty.phenotypes.phenotype_mutants()[source]

Return a dictionary { phenotype: set(mutant_objects for mutant), … }.