Module: rje_motif Description: Motif Class and Methods Module Version: 3.1 Last Edit: 04/06/14

Copyright © 2006 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje

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

Function

This module contains the Motif class for use with both Slim Pickings and PRESTO, and associated methods. This basic Motif class stores its pattern in several forms: - info['Sequence'] stores the original pattern given to the Motif object - list['PRESTO'] stores the pattern in a list of PRESTO format elements, where each element is a discrete part of the motif pattern - list['Variants'] stores simple strings of all the basic variants - length and ambiguity - for indentifying the "best" variant for any given match - dict['Search'] stores the actual regular expression variants used for searching, which has a separate entry for each length variant - otherwise Python RegExp gets confused! Keys for this dictionary relate to the number of mismatches allowed in each variant.

The Motif Class is designed for use with the MotifList class. When a motif is added to a MotifList object, the Motif.format() command is called, which generates the 'PRESTO' list. After this - assuming it is to be kept - Motif.makeVariants() makes the 'Variants' list. If creating a motif object in another module, these method should be called before any sequence searching is performed. If mismatches are being used, the Motif.misMatches() method must also be called.

Commandline

These options should be listed in the docstring of the module using the motif class:
- alphabet=LIST : List of letters in alphabet of interest [AAs]
- ambcut=X : Cut-off for max number of choices in ambiguous position to be shown as variant (0=All) [10]
- trimx=T/F : Trims Xs from the ends of a motif [False]

History Module Version History

    # 2.0 - Revised version based on RJE_MOTIF 1.1 and bits of PRESTO 1.8.
    # 2.1 - Added "n of m" style elements in the form 
    # 2.2 - AmbCut now limits the number of ambiguous choices when compare=T
    # 2.3 - Added Information Content Methods
    # 2.4 - Added defineMotif method
    # 2.5 - Added reformatMiniMotif method
    # 3.0 - Reworked for use with MotifList and MotifOcc objects. Add Expect dictionary.
    # 3.1 - Fixed minor code bugs.