Module: SLiMSuite Description: Short Linear Motif analysis Suite Version: 1.11.0 Last Edit: 06/04/21 Citation: Edwards et al. (2020), Methods Mol Biol. 2141:37-72. Old citation: Edwards RJ & Palopoli N (2015): Methods Mol Biol. 1268:89-141. [PMID: 25555723]

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 slimparser 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. See rje for general commands.

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:
- PeptCluster = peptcluster.PeptCluster. Peptide alignment, pairwise distance and clustering tool.
- QSLiMFinder = qslimfinder.QSLiMFinder. Query-based Short Linear Motif Finder - de novo SLiM prediction.
- SLiMBench = slimbench.SLiMBench. SLiM discovery benchmarking module.
- SLiMCore = rje_slimcore.SLiMCore. SLiMSuite core module with MegaSLiM and UPC functions.
- SLiMFarmer = slimfarmer.SLiMFarmer. SLiMSuite job forking/HPC controller.
- SLiMFinder = slimfinder.SLiMFinder. Short Linear Motif Finder - de novo SLiM prediction.
- SLiMList = rje_slimlist.SLiMList. Short Linear Motif manipulation/filtering module.
- SLiMMaker = slimmaker.SLiMMaker. Simple SLiM generation from aligned peptide sequences.
- SLiMMutant = slimmutant.SLiMMutant. Short Linear Motif Mutation Analysis Tool
- SLiMParser - slimparser.SLiMParser. SLiMSuite REST output parsing tool.
- SLiMProb = slimprob.SLiMProb. Short Linear Motif Probability - known SLiM prediction.

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]
test=T/F # Trigger test function for program X, if implemented. If prog=test a general test will run. [False]
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.
    # 1.7.1 - Added error raising for protected REST alias data.
    # 1.8.0 - Added BUSCOMP and basic test function.
    # 1.8.1 - Updated documentation and added IUPred2. General tidy up and new example data for protocols paper.
    # 1.9.0 - Added SAAGA, Diploidocus, SynBad and Genomics. Slight module tidy for GitHub updates.
    # 1.9.1 - Added SLiMParser and SLiMMutant to wrapped tools to match documentation.
    # 1.10.0- Various program updates: see release_notes.txt.
    # 1.11.0- SeqSuite added DepthSizer and DepthKopy.