Package Bio :: Package NeuralNetwork :: Package Gene :: Module Signature :: Class SignatureFinder
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Class 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.
Method Summary
  __init__(self, alphabet_strict)
Initialize a finder to get signatures.
  find(self, seq_records, signature_size, max_gap)
Find all signatures in a group of sequences.
  _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.

Method Details

__init__(self, alphabet_strict=1)
(Constructor)

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(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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