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Find motifs in a set of Sequence Records.
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Initialize a finder to get motifs. Arguments: o alphabet_strict - Whether or not motifs should be restricted to having all of there elements within the alphabet of the sequences. This requires that the Sequences have a real alphabet, and that all sequences have the same alphabet. |
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). |
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. |
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. |
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