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

Class SchemaFinder

object --+
         |
        SchemaFinder

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())
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

find(self, seq_records)
Find well-represented schemas in the given set of SeqRecords.

source code

find_differences(self, first_records, second_records)
Find schemas which differentiate between the two sets of SeqRecords.

source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, num_schemas=100, schema_finder=GeneticAlgorithmFinder())
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

Class SchemaFinder

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

init(self, num_schemas=100, schema_finder=GeneticAlgorithmFinder())
(Constructor)