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


Find motifs in a set of Sequence Records.
Method Summary
  __init__(self, alphabet_strict)
Initialize a finder to get motifs.
  find(self, seq_records, motif_size)
Find all motifs of the given size in the passed SeqRecords.
  find_differences(self, first_records, second_records, motif_size)
Find motifs in two sets of records and return the differences.
  _add_motif(self, motif_dict, motif_to_add)
Add a motif to the given dictionary.
  _get_motif_dict(self, seq_records, motif_size)
Return a dictionary with information on motifs.

Method Details

__init__(self, alphabet_strict=1)
(Constructor)

Initialize a finder to get motifs.

Arguments:

o alphabet_strict - Whether or not motifs should be restricted to having all of there elements within the alphabet of the sequences. This requires that the Sequences have a real alphabet, and that all sequences have the same alphabet.

find(self, seq_records, motif_size)

Find all motifs of the given size in the passed SeqRecords.

Arguments:

o seq_records - A list of SeqRecord objects which the motifs will be found from.

o motif_size - The size of the motifs we want to look for.

Returns: A PatternRepository object that contains all of the motifs (and their counts) found in the training sequences).

find_differences(self, first_records, second_records, motif_size)

Find motifs in two sets of records and return the differences.

This is used for finding motifs, but instead of just counting up all of the motifs in a set of records, this returns the differences between two listings of seq_records.

o first_records, second_records - Two listings of SeqRecord objects to have their motifs compared.

o motif_size - The size of the motifs we are looking for.

Returns: A PatternRepository object that has motifs, but instead of their raw counts, this has the counts in the first set of records subtracted from the counts in the second set.

_add_motif(self, motif_dict, motif_to_add)

Add a motif to the given dictionary.

_get_motif_dict(self, seq_records, motif_size)

Return a dictionary with information on motifs.

This internal function essentially does all of the hard work for finding motifs, and returns a dictionary containing the found motifs and their counts. This is internal so it can be reused by find_motif_differences.

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