Package Bio :: Package NeuralNetwork :: Package Gene :: Module Motif :: Class MotifCoder
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Class MotifCoder


Convert motifs and a sequence into neural network representations.

This is designed to convert a sequence into a representation that can be fed as an input into a neural network. It does this by representing a sequence based the motifs present.
Method Summary
  __init__(self, motifs)
Initialize an input producer with motifs to look for.
  representation(self, sequence)
Represent a sequence as a set of motifs.

Method Details

__init__(self, motifs)
(Constructor)

Initialize an input producer with motifs to look for.

Arguments:

o motifs - A complete list of motifs, in order, that are to be searched for in a sequence.

representation(self, sequence)

Represent a sequence as a set of motifs.

Arguments:

o sequence - A Bio.Seq object to represent as a motif.

This converts a sequence into a representation based on the motifs. The representation is returned as a list of the relative amount of each motif (number of times a motif occured divided by the total number of motifs in the sequence). The values in the list correspond to the input order of the motifs specified in the initializer.

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