biopython v1.71.0 Bio.NeuralNetwork.Gene.Schema.SchemaCoder
Convert a sequence into a representation of ambiguous motifs (schemas).
This takes a sequence, and returns the number of times specified motifs are found in the sequence. This lets you represent a sequence as just a count of (possibly ambiguous) motifs.
Link to this section Summary
Initialize the coder to convert sequences
Represent the given input sequence as a bunch of motif counts
Link to this section Functions
Link to this function __init__()
Initialize the coder to convert sequences.
- schema - A list of all of the schemas we want to search for in input sequences.
- ambiguous_converter - An Schema class which can be used to convert motifs into regular expressions for searching.
Link to this function representation()
Represent the given input sequence as a bunch of motif counts.
- sequence - A Bio.Seq object we are going to represent as schemas.
This takes the sequence, searches for the motifs within it, and then returns counts specifying the relative number of times each motifs was found. The frequencies are in the order the original motifs were passed into the initializer.