Module: RJE_SLiMHTML Description: Module for generating HTML for Human SLiMFinder study Version: 0.9 Last Edit: 11/03/11

Copyright © 2010 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_ensembl rje_go rje_ppi rje_seq rje_sequence rje_slim rje_svg rje_uniprot rje_zen rje_dismatrix_V2 rje_tree rje_xgmml happi slimfinder

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

Function

The function of this module will be added here.

Commandline

datapath=PATH : Path to parent data directory [./]
htmlpath=PATH : Path of parent html directory [./html]
stylesheets=LIST : List of CSS files to use ['../example.css','../redwards.css']
border=X : Border setting for tables [0]
dropfields=LIST : Fields to exclude from summary tables []
fakehtml=T/F : Whether to make UniFake HTML [True]
unifake=PATH : Path to UniFake dat file(s) [./unifake/]
unipath=PATH : Path to real UniProt dat file(s) [./uniprot/]
unireal=LIST : Real UniProt data to add to UniFake output (Empty=None) [AC,GN,RC,RX,CC,DR,PE,KW,FT]
makepng=T/F : Whether to (look for and) make PNG files with R [True]
svg=T/F : Make SVG files rather than PNG files [True]
addrand=T/F : Whether to add pages for random data [True]
makepages=LIST : Types of pages to make [front,gene,domain,rand,slim,fake,occaln,interactome,slimaln,go,nested]
titletext=FILE : File containing (Page,ID,Title) [titletext.tdt]
slimdesc=FILE : File containing descriptions for SLiMs [slimdesc.txt]
baddset=LIST : List of Bad Datasets to filter out of main and occ database tables []
pround=T/F : Whether to round off occurrence positions for PNGs [True]
xgcut=X : Significance cut-off for XGMML [0.01]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.3 - Added code for making Random Dataset pages
    # 0.4 - Updated UPC pages and added additional front pages.
    # 0.5 - Split front page into front and full. Added GO tabs/pages.
    # 0.6 - Added XGMML output.
    # 0.7 - Modified output for HumSF10 and HAPPI analysis.
    # 0.8 - Added SVG output. Integrated better with HAPPI code.
    # 0.9 - Added SLiM Descriptions.