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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.
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Initialize a finder to get signatures. Arguments: o 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. |
Find all signatures in a group of sequences. Arguments: o seq_records - A list of SeqRecord objects we'll use the sequences from to find signatures. o signature_size - The size of each half of a signature (ie. if this is set at 3, then the signature could be AGC-----GAC) o max_gap - The maximum gap size between two parts of a signature. |
Return a dictionary with all signatures and their counts. This internal function does all of the hard work for the find_signatures function. |
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