Evolife.Genetics.Genetic_map.Genetic_map Class Reference

a Genetic_map is a series of genes, located one after the other More...

Inheritance diagram for Evolife.Genetics.Genetic_map.Genetic_map:

Public Member Functions
def	__init__ (self, GeneMap)
	just calls init_genes More...
def	init_genes (self, gene_list)
	creates genes and puts them into 'GeneMap' Accepted syntax: ['genename1', 'genename2',...]: lengths and coding are retrieved from configuration. More...
def	get_gene (self, locus)
	returns GeneMap[locus] More...
def	get_locus (self, gene_name)
	returns the gene's locus More...
def	get_gene_name (self, locus)
	finds the name of the gene at locus More...
def	get_gene_names (self)
	returns genes' names as a list More...
def	get_gene_boundaries (self, locus)
	finds the gene's boundaries on the DNA More...
def	get_coding (self, locus)
	returns the gene's coding type (weighted, unweighted, ...) More...
def	gene_boundaries (self, gene_name)
	finds the gene's boundaries on the DNA More...
def	geneMap_length (self)
	location of the end of the last gene on Genemap More...
def	locus_range (self, Locus)
	returns the maximal amplitude of the gene at Locus More...
def	gene_range (self, gene_name)
	returns the maximal amplitude of the gene More...
def	gene_pattern (self)
	returns a binary mask showing gene alternation on DNA More...

Public Attributes
	GeneMap

Detailed Description

a Genetic_map is a series of genes, located one after the other

Definition at line 51 of file Genetic_map.py.

Constructor & Destructor Documentation

__init__()

def Evolife.Genetics.Genetic_map.Genetic_map.__init__	(		self,
			GeneMap
	)

just calls init_genes

Reimplemented in Evolife.Genetics.Genetic_map.GMTest, Evolife.Scenarii.CustomScenario.Scenario, and Evolife.Scenarii.Default_Scenario.Default_Scenario.

Definition at line 54 of file Genetic_map.py.

Member Function Documentation

gene_boundaries()

def Evolife.Genetics.Genetic_map.Genetic_map.gene_boundaries	(		self,
			gene_name
	)

finds the gene's boundaries on the DNA

Definition at line 125 of file Genetic_map.py.

gene_pattern()

def Evolife.Genetics.Genetic_map.Genetic_map.gene_pattern

(

self

)

returns a binary mask showing gene alternation on DNA

Definition at line 155 of file Genetic_map.py.

gene_range()

def Evolife.Genetics.Genetic_map.Genetic_map.gene_range	(		self,
			gene_name
	)

returns the maximal amplitude of the gene

Definition at line 150 of file Genetic_map.py.

geneMap_length()

def Evolife.Genetics.Genetic_map.Genetic_map.geneMap_length

(

self

)

location of the end of the last gene on Genemap

Definition at line 130 of file Genetic_map.py.

get_coding()

def Evolife.Genetics.Genetic_map.Genetic_map.get_coding	(		self,
			locus
	)

returns the gene's coding type (weighted, unweighted, ...)

Definition at line 120 of file Genetic_map.py.

get_gene()

def Evolife.Genetics.Genetic_map.Genetic_map.get_gene	(		self,
			locus
	)

returns GeneMap[locus]

Definition at line 88 of file Genetic_map.py.

get_gene_boundaries()

def Evolife.Genetics.Genetic_map.Genetic_map.get_gene_boundaries	(		self,
			locus
	)

finds the gene's boundaries on the DNA

Definition at line 115 of file Genetic_map.py.

get_gene_name()

def Evolife.Genetics.Genetic_map.Genetic_map.get_gene_name	(		self,
			locus
	)

finds the name of the gene at locus

Definition at line 105 of file Genetic_map.py.

get_gene_names()

def Evolife.Genetics.Genetic_map.Genetic_map.get_gene_names

(

self

)

returns genes' names as a list

Definition at line 110 of file Genetic_map.py.

get_locus()

def Evolife.Genetics.Genetic_map.Genetic_map.get_locus	(		self,
			gene_name
	)

returns the gene's locus

Definition at line 96 of file Genetic_map.py.

init_genes()

def Evolife.Genetics.Genetic_map.Genetic_map.init_genes	(		self,
			gene_list
	)

creates genes and puts them into 'GeneMap' Accepted syntax: ['genename1', 'genename2',...]: lengths and coding are retrieved from configuration.

[('genename1', 8), ('genename2', 4),...]: numbers give lengths in bits; coding is retrieved from configuration. [('genename1', 8, 'Weighted'), ('genename2', 4, 'Unweighted'),...]: coding can be 'Weighted', 'Unweighted', 'Gray', 'NoCoding'. Note that 'Unweighted' is unsuitable to explore large space.

Definition at line 59 of file Genetic_map.py.

locus_range()

def Evolife.Genetics.Genetic_map.Genetic_map.locus_range	(		self,
			Locus
	)

returns the maximal amplitude of the gene at Locus

Definition at line 135 of file Genetic_map.py.

Member Data Documentation

GeneMap

Evolife.Genetics.Genetic_map.Genetic_map.GeneMap

Definition at line 67 of file Genetic_map.py.

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The documentation for this class was generated from the following file:

• Genetics/Genetic_map.py