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Package Bio :: Package NeuralNetwork :: Package Gene :: Module Signature :: Class SignatureFinder |
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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.Method Summary | |
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Initialize a finder to get signatures. | |
Find all signatures in a group of sequences. | |
Add a signature to the given dictionary. | |
Return a dictionary with all signatures and their counts. |
Method Details |
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__init__(self,
alphabet_strict=1)
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find(self, seq_records, signature_size, max_gap)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. |
_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. |
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