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])
['cbfA']
>>> # List a set of all phenotypes referenced by a single mutant
>>> print mutant_phenotypes(dicty_mutants[0])
['aberrant protein localization']

Classes and Functions

class orangecontrib.bio.dicty.phenotypes.DictyMutant(mutant_entry)

A single Dictyostelium discoideum mutant from the Dictybase.

Parameters:

mutant_entry (str) – A single mutant entry from curated mutants file.

Variables:
  • DictyMutant.name – dictyBase ID.
  • DictyMutant.descriptor – dictyBase strain descriptor.
  • DictyMutant.genes – all associated genes.
  • DictyMutant.phenotypes – all associated phenotypes.
class orangecontrib.bio.dicty.phenotypes.DictyMutants(local_database_path=None)

A collection of Dictybase mutants as a dictionary of DictyMutant objects.

Parameters:local_database_path – A path for storing D. dictyostelium mutants objects. If None then a default database path is used.
orangecontrib.bio.dicty.phenotypes.mutants()

Return all DictyMutant objects.

orangecontrib.bio.dicty.phenotypes.genes()

Return a set of all genes referenced in the Dictybase.

orangecontrib.bio.dicty.phenotypes.phenotypes()

Return a set of all phenotypes referenced in Dictybase.

orangecontrib.bio.dicty.phenotypes.mutant_genes(mutant)

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

orangecontrib.bio.dicty.phenotypes.mutant_phenotypes(mutant)

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

orangecontrib.bio.dicty.phenotypes.gene_mutants()

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

orangecontrib.bio.dicty.phenotypes.phenotype_mutants()

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