Evolife documentation

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Module Evolife.Genetics.Genetic_map:        
===================================
EVOLIFE: Module Genetic_map:
        Definition of genes as DNA segment having semantics
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    **************************************************************************************
    Class Gene_def:        
    ==============
    definition of semantic segments on DNA.
        A gene is a geographical entity: start_position, end_position, length...
    **************************************************************************************

        ----------------------------------------------------------------------------------
        Method Gene_def.__init__:        
        ========================
        A gene knows its name, its length,
            its locus (order in the list of genes) and its start and end position
            on the DNA
        ----------------------------------------------------------------------------------
        Arguments:
            . gene_name
            . gene_length
            . locus
            . position
            . coding


    **************************************************************************************
    Class Genetic_map:        
    =================
    a Genetic_map is a series of genes, located one after the other
    **************************************************************************************

        ----------------------------------------------------------------------------------
        Method Genetic_map.__init__:        
        ===========================
        just calls init_genes
        ----------------------------------------------------------------------------------
        Arguments:
            . GeneMap


        ----------------------------------------------------------------------------------
        Method Genetic_map.init_genes:        
        =============================
        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.
        ----------------------------------------------------------------------------------
        Arguments:
            . gene_list


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_gene:        
        ===========================
        returns GeneMap[locus]
        ----------------------------------------------------------------------------------
        Arguments:
            . locus


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_locus:        
        ============================
        returns the gene’s locus
        ----------------------------------------------------------------------------------
        Arguments:
            . gene_name


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_gene_name:        
        ================================
        finds the name of the gene at locus
        ----------------------------------------------------------------------------------
        Arguments:
            . locus


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_gene_names:        
        =================================
        returns genes’ names as a list
        ----------------------------------------------------------------------------------


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_gene_boundaries:        
        ======================================
        finds the gene’s boundaries on the DNA
        ----------------------------------------------------------------------------------
        Arguments:
            . locus


        ----------------------------------------------------------------------------------
        Method Genetic_map.get_coding:        
        =============================
        returns the gene’s coding type (weighted, unweighted, ...)
        ----------------------------------------------------------------------------------
        Arguments:
            . locus


        ----------------------------------------------------------------------------------
        Method Genetic_map.gene_boundaries:        
        ==================================
        finds the gene’s boundaries on the DNA
        ----------------------------------------------------------------------------------
        Arguments:
            . gene_name


        ----------------------------------------------------------------------------------
        Method Genetic_map.geneMap_length:        
        =================================
        location of the end of the last gene on Genemap
        ----------------------------------------------------------------------------------


        ----------------------------------------------------------------------------------
        Method Genetic_map.locus_range:        
        ==============================
        returns the maximal amplitude of the gene at Locus
        ----------------------------------------------------------------------------------
        Arguments:
            . Locus


        ----------------------------------------------------------------------------------
        Method Genetic_map.gene_range:        
        =============================
        returns the maximal amplitude of the gene
        ----------------------------------------------------------------------------------
        Arguments:
            . gene_name


        ----------------------------------------------------------------------------------
        Method Genetic_map.gene_pattern:        
        ===============================
        returns a binary mask showing gene alternation on DNA
        ----------------------------------------------------------------------------------


    

    

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