Module: rje_motifocc Description: Motif Occurrence Module Version: 0.0 Last Edit: 29/01/07

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: rje rje_seq

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See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module contains the MotifOcc class. This class if for storing methods and attributes pertinent to an individual occurrence of a motif, i.e. one Motif instance in one sequence at one position. This class is loosely based on (and should replace) the old PRESTO PrestoHit object. (And, to some extent, the PrestoSeqHit object.) This class is designed to be flexible for use with PRESTO, SLiMPickings and CompariMotif, among others.

In addition to storing the standard info and stat dictionaries, this object will store a "Data" dictionary, which contains the (program-specific) data to be output for a given motif. All data will be in string format. The getData() and getStat() methods will automatically convert from string to numerics as needed.

Commandline

This module has no standalone functionality and should not be called from the commandline.