__init__ ( self,  ambiguity_info )

Initialize with ambiguity information.

Arguments:

• ambiguity_info - A dictionary which maps letters in the motifs to the ambiguous characters which they might represent. For example, {R : 'AG'} specifies that Rs in the motif can match a A or a G. All letters in the motif must be represented in the ambiguity_info dictionary.

all_unambiguous ( self )

Return a listing of all unambiguous letters allowed in motifs.

encode_motif ( self,  motif )

Encode the passed motif as a regular expression pattern object.

Arguments:

• motif - The motif we want to encode. This should be a string.

Returns: A compiled regular expression pattern object that can be used for searching strings.

find_ambiguous ( self,  motif )

Return the location of ambiguous items in the motif.

This just checks through the motif and compares each letter against the ambiguity information. If a letter stands for multiple items, it is ambiguous.

find_matches (
        self,
        motif,
        query,
        )

Return all non-overlapping motif matches in the query string.

This utilizes the regular expression findall function, and will return a list of all non-overlapping occurances in query that match the ambiguous motif.

num_ambiguous ( self,  motif )

Return the number of ambiguous letters in a given motif.

num_matches (
        self,
        motif,
        query,
        )

Find the number of non-overlapping times motif occurs in query.