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rje_seqplot V0.0

Sequence plotting module

Module: rje_seqplot
Description: Sequence plotting module
Version: 0.0
Last Edit: 16/06/08

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_disorder rje_seq rje_slimcalc rje_zen


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

Function

This module is designed to work in conjunction with Norman's sequence plotting tool(s).

See also rje_seq, rje_uniprot and rje_disorder options.

Commandline

INPUT OPTIONS

seqin=FILE : File containing input sequences [None]
occfile=FILE : File containing motif occurrences to plot [None]
plotstat=LIST : List of stats to plot (cons/rel/dis/sa/hyd) [cons/rel/dis]
plotft=LIST : List of features to plot if input is UniProt [SIGNALP,TRANSMEMBRANE,DOMAIN,PFAM]
plotre=LIST : List of regular expressions to plot []
plotwin=X : Window for stats plot +/- [7]

OUTPUT OPTIONS

outfile=X : Leader for output files [None]
occonly=T/F : Only output sequences with motif occurrences [False]
rescale=T/F : Whether to rescale plotstats (Truncate at 0.0 and normalise to max 1.0) [True]

History Module Version History

    # 0.0 - Initial Compilation.

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