__init__ ( self,  alphabet_strict=1 )

Initialize a finder to get motifs.

Arguments:

• 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.

_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.

find (
        self,
        seq_records,
        motif_size,
        )

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

Arguments:

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

• 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.

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

• 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.