Package Bio :: Package NeuralNetwork :: Package Gene :: Module Schema :: Class SchemaFinder
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Class SchemaFinder

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object --+

Find schema in a set of sequences using a genetic algorithm approach.

Finding good schemas is very difficult because it takes forever to enumerate all of the potential schemas. This finder using a genetic algorithm approach to evolve good schema which match many times in a set of sequences.

The default implementation of the finder is ready to find schemas in a set of DNA sequences, but the finder can be customized to deal with any type of data.

Instance Methods [hide private]
__init__(self, num_schemas=100, schema_finder=GeneticAlgorithmFinder())
Initialize the Schema Finder with its parameters.
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find(self, seq_records)
Find well-represented schemas in the given set of SeqRecords.
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find_differences(self, first_records, second_records)
Find schemas which differentiate between the two sets of SeqRecords.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, num_schemas=100, schema_finder=GeneticAlgorithmFinder())

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Initialize the Schema Finder with its parameters.

  • num_schemas -- the number of useful (positive fitness) schemas we want to generate.
Overrides: object.__init__