__init__ ( self,  alphabet_strict=1 )

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.

_add_sig (
        self,
        sig_dict,
        sig_to_add,
        )

Add a signature to the given dictionary.

_get_signature_dict (
        self,
        seq_records,
        sig_size,
        max_gap,
        )

Return a dictionary with all signatures and their counts.

This internal function does all of the hard work for the find_signatures function.

find (
        self,
        seq_records,
        signature_size,
        max_gap,
        )

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.