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SLiMSuite V1.7.0

Short Linear Motif analysis Suite

Module: SLiMSuite
Description: Short Linear Motif analysis Suite
Version: 1.7.0
Last Edit: 16/02/17
Citation: Edwards RJ & Palopoli N (2015): Methods Mol Biol. 1268:89-141.

Copyright © 2014 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_obj rje_slimcore rje_slimlist comparimotif_V3 seqsuite qslimfinder slimbench slimfarmer slimfinder slimmaker slimprob slimmutant gablam gopher haqesac multihaq peptcluster pingu_V4 presto_V5 badasp budapest fiesta gasp gfessa picsi unifake seqmapper seqforker rje_seqgen


See SLiMSuite Blog for further documentation.

Function

SLiMSuite is designed to be a front end for the SLiMSuite set of sequence analysis tools. The relevant tool is given by the first system command, or selected using prog=X (or program=X). As much as possible, SLiMSuite will emulate running that tool from the commandline, adding any matching X.ini file to the default commandline options read in (*before* settings read from slimsuite.ini itself). By default, the SLiMCore tool will be called (libraries/rje_slimcore.py) and read in commands from slimcore.ini.

Help for the selected tool can be accessed using the help=T option. Note that -h, -help or help alone will trigger the SLiMSuite help (this!). As -help or help will also set help=T, these commands will trigger both the SLiMSuite help and the selected program help (unless over-ruled by help=F). An explicit help=T command will only trigger the selected program help.

Running SLiMSuite should also try importing all the main SLiMSuite modules, testing for download errors etc.

SLiMSuite tools

The list of tools recognised by prog=X will be added here as the relevant code is added:
- SLiMCore = rje_slimcore.SLiMCore. SLiMSuite core module with MegaSLiM and UPC functions.
- SLiMFarmer = slimfarmer.SLiMFarmer. SLiMSuite job forking/HPC controller.
- QSLiMFinder = qslimfinder.QSLiMFinder. Query-based Short Linear Motif Finder - de novo SLiM prediction.
- SLiMFinder = slimfinder.SLiMFinder. Short Linear Motif Finder - de novo SLiM prediction.
- SLiMList = rje_slimlist.SLiMList. Short Linear Motif manipulation/filtering module.
- SLiMProb = slimprob.SLiMProb. Short Linear Motif Probability - known SLiM prediction.
- SLiMBench = slimbench.SLiMBench. SLiM discovery benchmarking module.
- SLiMMaker = slimmaker.SLiMMaker. Simple SLiM generation from aligned peptide sequences.
- PeptCluster = peptcluster.PeptCluster. Peptide alignment, pairwise distance and clustering tool.

Example use to run SLiMFinder

python SLiMSuitePATH/tools/slimsuite.py slimfinder

Please also see the SeqSuite documentation for additional utilities, which can be run from SLiMSuite or SeqSuite.

Commandline


prog=X # Identifies the tool to be used. Will load defaults from X.ini (before slimsuite.ini) [help]
help=T/F # Return the help documentation for program X. [False]


See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation based on SeqSuite.
    # 1.0 - Moved to tools/ for general release. Added reading and using of SeqSuite programs.
    # 1.1 - Added slimlist.
    # 1.2 - Added SLiMBench.
    # 1.3.0 - Added SLiMMaker and modified code to work with REST services.
    # 1.4.0 - Added RLC and Disorder progs to call SLiMCore. Added CompariMotif.
    # 1.5.0 - Added peptcluster and peptalign calls.
    # 1.5.1 - Changed disorder to iuscore to avoid module conflict.
    # 1.5.2 - Updated XRef REST call.
    # 1.6.0 - Removed SLiMCore as default. Default will now show help.
    # 1.7.0 - Updated to work with symbolic link in main slimsuite/ path.

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