biopython v1.71.0 Bio.NeuralNetwork.Gene.Signature.SignatureFinder
Find Signatures in a group of sequence records.
In this simple implementation, signatures are just defined as a two motifs separated by a gap. We need something a lot smarter than this to find more complicated signatures.
Link to this section Summary
Functions
Initialize a finder to get signatures
Add a signature to the given dictionary
Return a dictionary with all signatures and their counts
Find all signatures in a group of sequences
Link to this section Functions
Link to this function
__init__()
Initialize a finder to get signatures.
Arguments:
- alphabet_strict - Specify whether signatures should be required to have all letters in the signature be consistent with the alphabet of the original sequence. This requires that all Seqs used have a consistent alphabet. This helps protect against getting useless signatures full of ambiguity signals.
Link to this function
_add_sig()
Add a signature to the given dictionary.
Link to this function
_get_signature_dict()
Return a dictionary with all signatures and their counts.
This internal function does all of the hard work for the find_signatures function.
Link to this function
find()
Find all signatures in a group of sequences.
Arguments:
- seq_records - A list of SeqRecord objects we’ll use the sequences from to find signatures.
- signature_size - The size of each half of a signature (ie. if this is set at 3, then the signature could be AGC——-GAC)
- max_gap - The maximum gap size between two parts of a signature.