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python-biopython  1.60
Public Member Functions | Public Attributes | Private Attributes
Bio.NeuralNetwork.Gene.Schema.SchemaFinder Class Reference

List of all members.

Public Member Functions

def __init__
def find
def find_differences

Public Attributes


Private Attributes


Detailed Description

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.

Definition at line 439 of file

Constructor & Destructor Documentation

def Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__ (   self,
  num_schemas = 100,
  schema_finder = GeneticAlgorithmFinder() 

Definition at line 452 of file

00453                  schema_finder = GeneticAlgorithmFinder()):
00454         self.num_schemas = num_schemas
00455         self._finder = schema_finder
00457         self.evaluator = Schema(self._finder.alphabet.alphabet_matches)

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Member Function Documentation

def Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find (   self,
Find well-represented schemas in the given set of SeqRecords.

Definition at line 458 of file

00459     def find(self, seq_records):
00460         """Find well-represented schemas in the given set of SeqRecords.
00461         """
00462         fitness_evaluator = MostCountSchemaFitness(seq_records,
00463                                                    self.evaluator)
00465         return self._finder.find_schemas(fitness_evaluator.calculate_fitness,
00466                                          self.num_schemas)

def Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find_differences (   self,
Find schemas which differentiate between the two sets of SeqRecords.

Definition at line 467 of file

00468     def find_differences(self, first_records, second_records):
00469         """Find schemas which differentiate between the two sets of SeqRecords.
00470         """
00471         fitness_evaluator = DifferentialSchemaFitness(first_records,
00472                                                       second_records,
00473                                                       self.evaluator)
00475         return self._finder.find_schemas(fitness_evaluator.calculate_fitness,
00476                                          self.num_schemas)

Member Data Documentation

Definition at line 454 of file

Definition at line 456 of file

Definition at line 453 of file

The documentation for this class was generated from the following file: