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Module Evolife.Genetics.Genetic_map:
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EVOLIFE: Module Genetic_map:
Definition of genes as DNA segment having semantics
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Class Gene_def:
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definition of semantic segments on DNA.
A gene is a geographical entity: start_position, end_position, length...
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Method Gene_def.__init__:
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A gene knows its name, its length,
its locus (order in the list of genes) and its start and end position
on the DNA
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Arguments:
. gene_name
. gene_length
. locus
. position
. coding
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Class Genetic_map:
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a Genetic_map is a series of genes, located one after the other
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Method Genetic_map.__init__:
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just calls init_genes
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Arguments:
. GeneMap
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Method Genetic_map.init_genes:
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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.
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Arguments:
. gene_list
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Method Genetic_map.get_gene:
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returns GeneMap[locus]
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Arguments:
. locus
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Method Genetic_map.get_locus:
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returns the gene’s locus
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Arguments:
. gene_name
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Method Genetic_map.get_gene_name:
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finds the name of the gene at locus
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Arguments:
. locus
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Method Genetic_map.get_gene_names:
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returns genes’ names as a list
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Method Genetic_map.get_gene_boundaries:
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finds the gene’s boundaries on the DNA
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Arguments:
. locus
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Method Genetic_map.get_coding:
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returns the gene’s coding type (weighted, unweighted, ...)
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Arguments:
. locus
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Method Genetic_map.gene_boundaries:
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finds the gene’s boundaries on the DNA
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Arguments:
. gene_name
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Method Genetic_map.geneMap_length:
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location of the end of the last gene on Genemap
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Method Genetic_map.locus_range:
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returns the maximal amplitude of the gene at Locus
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Arguments:
. Locus
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Method Genetic_map.gene_range:
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returns the maximal amplitude of the gene
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Arguments:
. gene_name
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Method Genetic_map.gene_pattern:
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returns a binary mask showing gene alternation on DNA
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