Package Bio :: Package NeuralNetwork :: Package Gene :: Module Pattern :: Class PatternIO
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Class PatternIO


Allow reading and writing of patterns to files.

This just defines a simple persistance class for patterns, making it easy to write them to a file and read 'em back.
Method Summary
  __init__(self, alphabet)
Intialize the reader and writer class.
  read(self, input_handle)
Read patterns from the specified handle.
  write(self, pattern_list, output_handle)
Write a list of patterns to the given handle.
  write_seq(self, seq_pattern_list, output_handle)
Convenience function to write Seq objects to a file.

Method Details

__init__(self, alphabet=None)
(Constructor)

Intialize the reader and writer class.

Arguments:

o alphabet - An optional argument specifying the alphabet which patterns should follow. If an alphabet is set it'll be used to verify that all patterns follow it.

Attributes: o separator - A character to use in separating items in a signature when it is written to a file and read back. This character should not be in the possible alphabet of the sequences, or there will be trouble.

read(self, input_handle)

Read patterns from the specified handle.

write(self, pattern_list, output_handle)

Write a list of patterns to the given handle.

write_seq(self, seq_pattern_list, output_handle)

Convenience function to write Seq objects to a file.

This can take Seqs and MutableSeqs, and write them to a file as strings.

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