Module: SLiMJIM Description: Short Linear Motif Jolly Image Maker Version: 2.0 Last Edit: 08/09/10

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

Imported modules: rje rje_dismatrix_V2 rje_ensembl rje_genemap rje_go rje_slim rje_tree rje_seq rje_sequence rje_uniprot rje_zen

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

Function

This program is designed to be used in conjunction with the slimjim.r R script to generate useful images for helping the interpretation of SLiMFinder runs. These can be embedded into a series of linked html pages for ease of navigat- ion and data exploration.

Alternatively, SLiMJIM can be used to generate single images for single SLiMFinder runs, without the extra linking and PPI information.

Commandline

SLiMFinder Run Input Options

resfile=FILE : Main SLiMFinder results file []
resdir=PATH : Path to extra SLiMFinder results []
alndir=PATH : Path to orthologue alignments for those missing mapping.fas []
pairwise=FILE : Pingu Pairwise output file []
name=X : Name of analysis ['SLiMFinder Human PPI Analysis']
suffix=X : Suffix added to gene symbols for dataset name [.ppi]
ensgopath=PATH : Path to EnsGO files (!!! Restricted to Humans Currently !!!)
singlesf=FILE : Path to *.slimdb file for which to generate graphics for single run []

Specific Analysis Options

hublist=LIST : List of hub datasets to look at (*.ppi). Can use wildcards. []
runlist=LIST : Optional list to limit results to certain run IDs []
slimlist=LIST : Optional list to limit results to certain SLiMs []
runtypes=LIST : List of run types to generate output for (if multiple runs) []

Output Options

hubs=T/F : Whether to generate output for Hubs [True]
domains=T/F : Whether to generate output for Domains [True]
spokes=T/F : Whether to generate output for Spokes [True]
motifs=T/F : Whether to generate output for Motifs [True]
mains=T/F : Whether to generate main analysis pages [True]
makejim=T/F : Whether to generate data and PNG files [False]
jimdir=PATH : Output directory for generated PNG files [./]
mapdir=PATH : Output directory for intermediate composite *.mapping.fas files [sjmap/]
iridis=T/F : Whether running on IRIDIS - fork out R jobs [False]

HTML Output Options

makehtml=T/F : Whether to generate linked HTML output files [False]
htmlall=T/F : Whether to make HTML for all datasets or only those identified with hublist [False]
htmldir=PATH : Output path for HTML files [html/]
htmlcss=X : File to be used for cascading style sheet (in */resource/)
htmlpng=X : Graphic for corner of header frames - links back to Home ['SBS_100.png']
unihtml=T/F : Generate missing linked HTML DAT files [True]
unipath=PATH : Path to indexed real UniProt DAT files []
unifake=PATH : Path to indexed UniFake DAT file []
unireal=LIST : Real UniProt data to add to UniFake output (Empty=None) [AC,GN,RC,RX,CC,DR,PE,KW,FT]
tableonly=T/F : Only make delimited text versions of tables, not all HTML files [False]

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Altered basis of all protein naming to be gene-based. Added more visualisations and UniProt data.
    # 0.2 - Tidied up management of Hubs and Spokes.
    # 0.3 - Added SingleSF mode and tidied some of R code.
    # 0.4 - Added use of rje_iridis and code from sfmap2png.
    # 1.0 - Basic functionality all present. Fixed ordering bug.
    # 1.1 - Added tableonly=T/F option.
    # 2.0 - Updated to handle multiple runs and domain datasets.