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rje_markov V2.2

RJE Module for protein sequence Markov Chain related gubbins

Module: rje_markov
Description: RJE Module for protein sequence Markov Chain related gubbins
Version: 2.2
Last Edit: 17/01/13

Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_seq rje_zen


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

Function

This module is designed to handle a number of things to do with amino acid frequencies and the like, including: - Observed and expected 1mer .. Xmer frequencies

Some old functions including 1mer .. Xmer counts per protein are now only found in V1.2.

Commandline

## General ##
seqin=FILE : File with input sequences [None]
alphabet=X,Y,..Z : List of letters in alphabet of interest
split=X : Splits file into numbered files of X sequences and recombines at end.
autoload=T/F : Whether to load sequences automatically. If False, will try memory-efficient seqlist handling [False]
aafreq=FILE : Generate expected 1mer frequencies from FILE of aafreq [None]
xmerfile=FILE : File from which to load Xmer counts and build suffix tree [None]
direction=X : Direction to read chains (fwd/bwd/both) [fwd]
sorted=T/F : Whether to use sorted xmer fragments to reduce memory requirements [False]
scap=T/F : Whether to use special SCAP sorting of xmers (sorts all but last aa) [False]
negvpos=X : Perform Negatives versus Positives analysis on X.* files [None]
## Output ##
markov=T/F : Whether to perform Markov Chain Analysis of observed vs Expected for Xmers [True]
[xmers=X,Y] : Deal with Xmers [upto Ymers] [1]

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Basic working model, with suffix tree
    # 1.1 - Added splitting. Committed to suffix tree. Removed autoload and suftree options.
    # 1.2 - Removed obs/exp calculation from output - can calculate it from frequencies. Removed redundant methods.
    # 2.0 - Added reverse reading of markov chains and general tidy up. Removed XCount method - use V1.2 for this.
    # 2.1 - Temp fixed suftree problem. Module needs a major overhaul! Still broken in places.
    # 2.2 - Minor modifications. Main methods still need checking/fixing.

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.