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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Methods
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__init__
repair
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__init__
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__init__ (
self,
ambig_finder,
num_ambiguous,
)
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
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repair ( self, organism )
Perform a repair to remove excess ambiguous genes.
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