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rje_slimlist V1.7.3

SLiM dataset manager

Module: rje_slimlist
Description: SLiM dataset manager
Version: 1.7.3
Last Edit: 12/06/15

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_db rje_obj rje_seq rje_slim rje_slimcalc rje_zen rje_motif_V3


See SLiMSuite Blog for further documentation.

Function

This module is a replace for the rje_motiflist module and contains the SLiMList class, a replacement for the MotifList class. The primary function of this class is to load and store a list of SLiMs and control generic SLiM outputs for such programs as SLiMSearch. This class also controls motif filtering according to features of the motifs and/or their occurrences.

Although not actually designed with standalone functionality in mind, as of V1.3 it is possible to load motifs (inc. downloading ELM), filter/process motifs and output data using motifout=FILE and motinfo=FILE if desired.

Commandline

### Basic Input/Output Options ###
motifs=FILE : File of input motifs/peptides [None]
Single line per motif format = 'Name Sequence #Comments' (Comments are optional and ignored)
Alternative formats include fasta, SLiMDisc output and raw motif lists.
"elm" will download, process and load ELM classes using the ELM API.
reverse=T/F : Reverse the motifs - good for generating a test comparison data set [False]
wildscram=T/F : Perform a wildcard spacer scrambling - good for generating a test comparison data set [False]
motifout=FILE : Name of output file for reformatted/filtered SLiMs (PRESTO format) [None]
ftout=T/F : Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs [*.features.tdt]
mismatch=LIST : List of X:Y pairs for mismatch dictionary, where X mismatches allowed for Y+ defined positions []
motinfo=FILE : Filename for output of motif summary table (if desired) [None]
dna=T/F : Whether motifs should be considered as DNA motifs [False]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

Advanced Input I

minpos=X : Min number of defined positions [0]
minfix=X : Min number of fixed positions for a motif to contain [0]
minic=X : Min information content for a motif (1 fixed position = 1.0) [0.0]
varlength=T/F : Whether to motifs can have flexible-length elements [True]
goodmotif=LIST : List of text to match in Motif names to keep (can have wildcards) []
nrmotif=T/F : Whether to remove redundancy in input motifs [False]

Advanced Input II

trimx=T/F : Trims Xs from the ends of a motif [False]
minimotif=T/F : Input file is in minimotif format and will be reformatted (PRESTO File format only) [False]
ambcut=X : Cut-off for max number of choices in ambiguous position to be shown as variant [10]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

Advanced Output I

slimcalc=LIST : List of additional statistics to calculate for occurrences - Cons,SA,Hyd,Fold,IUP,Chg []
winsize=X : Used to define flanking regions for stats. If negative, will use flanks *only* [0]
iupath=PATH : The full path to the IUPred exectuable [c:/bioware/iupred/iupred.exe]
iucut=X : Cut-off for IUPred results (0.0 will report mean IUPred score) [0.0]
iumethod=X : IUPred method to use (long/short) [short]
percentile=X : Percentile steps to return in addition to mean [0]
peptides=T/F : Whether to output peptide sequences based on motif and winsize [False]

Advanced Output II

usealn=T/F : Whether to search for and use alignemnts where present. [False]
gopher=T/F : Use GOPHER to generate missing orthologue alignments in alndir - see gopher.py options [False]
alndir=PATH : Path to alignments of proteins containing motifs [./] * Use forward slashes (/)
alnext=X : File extension of alignment files, accnum.X [aln.fas]
protalndir=PATH : Output path for Protein Alignments [ProteinAln/]
motalndir=PATH : Output path for Motif Alignments []
flanksize=X : Size of sequence flanks for motifs [30]
xdivide=X : Size of dividing Xs between motifs [10]
fullforce=T/F : Whether to force regeneration of alignments using GOPHER

Advanced Output III

  • * see rje_slimcalc.py documentation

  • #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added SLiMCalc object to replace rje_motif_stats.
    # 0.2 - Added DNA option.
    # 0.3 - Added wildcard spacer scrambling - good for generating a test comparison data set.
    # 0.4 - Added motif-splitting based on ("|") options.
    # 0.5 - Fixed minor typo bug.
    # 0.6 - Added reading of ELM classes download for motifs. Modified splitting functions to cope with non-wildcard runs.
    # 1.0 - Functional module with lower case motif splitting fixed and ? -> .{0,1} replacement.
    # 1.1 - Modified to work with GOPHER V3.0 for alignments.
    # 1.2 - Added some extra functions for CompariMotif Memsaver mode
    # 1.3 - Added auto-download of ELM data.
    # 1.4 - Modified code to be compatible with SLiMCore V2.x objects.
    # 1.5 - Added run() method for slimsuite.py compatibility. Improved split motif handling.
    # 1.6 - Modified to read in new ELM class download file with extra header information. Added varlength=T/F filter.
    # 1.6 - Modified so that filtering one element of a split motif removes all.
    # 1.7.0 - Added direct feeding of motif file content for loading (for REST servers).
    # 1.7.1 - Modified input to allow motif=X in additon to motifs=X.
    # 1.7.2 - Fixed bug that could not accept variable length motifs from commandline. Improved error message.
    # 1.7.3 - Fixed bug that could not accept variable length motifs from commandline. Improved error message.

rje_slimlist REST Output formats

There is currently no specific help available on REST output for this program. Run with &rest=help for general
options. Run with &rest=full to get full server output. Individual outputs can be identified/parsed:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
...


&rest=OUTFMT can then be used to retrieve individual parts of the output in future.

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