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Package Bio :: Package NeuralNetwork :: Package Gene :: Module Motif :: Class MotifFinder |
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Method Summary | |
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Initialize a finder to get motifs. | |
Find all motifs of the given size in the passed SeqRecords. | |
Find motifs in two sets of records and return the differences. | |
Add a motif to the given dictionary. | |
Return a dictionary with information on motifs. |
Method Details |
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__init__(self,
alphabet_strict=1)
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find(self, seq_records, motif_size)Find all motifs of the given size in the passed SeqRecords. Arguments: o seq_records - A list of SeqRecord objects which the motifs will be found from. o motif_size - The size of the motifs we want to look for. Returns: A PatternRepository object that contains all of the motifs (and their counts) found in the training sequences). |
find_differences(self, first_records, second_records, motif_size)Find motifs in two sets of records and return the differences. This is used for finding motifs, but instead of just counting up all of the motifs in a set of records, this returns the differences between two listings of seq_records. o first_records, second_records - Two listings of SeqRecord objects to have their motifs compared. o motif_size - The size of the motifs we are looking for. Returns: A PatternRepository object that has motifs, but instead of their raw counts, this has the counts in the first set of records subtracted from the counts in the second set. |
_add_motif(self, motif_dict, motif_to_add)Add a motif to the given dictionary. |
_get_motif_dict(self, seq_records, motif_size)Return a dictionary with information on motifs. This internal function essentially does all of the hard work for finding motifs, and returns a dictionary containing the found motifs and their counts. This is internal so it can be reused by find_motif_differences. |
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