biopython v1.71.0 Bio.GA.Repair.Stabilizing.AmbiguousRepair
Perform repair to reduce the number of Ambiguous genes in a genome.
In cases where ambiguous genes are allowed in a genome (for example, where you have a wild card character like ‘‘ that will match anything), these can come to dominate a genome since, really, the best fitness is someting like ‘**’. This repair protects against that by changing ambiguous characters into some non-ambiguous gene.
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__init__()
Initialize the repair class.
Arguments:
- ambig_finder - A class implementing the function find_ambiguous which will return a list of all ambiguous positions in a sequence. It also must have the function all_unambiguous, which will return all allowed unambiguous letters.
- num_ambiguous - The minimum number of ambiguous items that are allowed in a genome. If there are more than this present, repair will be performed.
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repair()
Perform a repair to remove excess ambiguous genes.