biopython v1.71.0 Bio.NeuralNetwork.Gene.Schema.Schema
Deal with motifs that have ambiguity characters in it.
This motif class allows specific ambiguity characters and tries to speed up finding motifs using regular expressions.
This is likely to be a replacement for the Schema representation, since it allows multiple ambiguity characters to be used.
Link to this section Summary
Functions
Initialize with ambiguity information
Return a listing of all unambiguous letters allowed in motifs
Encode the passed motif as a regular expression pattern object
Return the location of ambiguous items in the motif
Return all non-overlapping motif matches in the query string
Return the number of ambiguous letters in a given motif
Find the number of non-overlapping times motif occurs in query
Link to this section Functions
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 an A or a G. All letters in the motif must be represented in the ambiguity_info dictionary.
Return a listing of all unambiguous letters allowed in motifs.
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.
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.
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 occurrences in query that match the ambiguous motif.
Return the number of ambiguous letters in a given motif.
Find the number of non-overlapping times motif occurs in query.