Module: RJE_HM_HTML Description: Module for generating HTML for APHID enrichment study Version: 0.3 Last Edit: 04/11/10

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

Imported modules: rje rje_db rje_go rje_slim rje_zen rje_slimhtml rje_ppi rje_dismatrix_V2 rje_tree slimfinder

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

Function

This module makes a set of linked webpages for the H&M integrin tail analysis. It is based on, and heavily uses, the code for rje_slimhtml.

Commandline

datapath=PATH : Path to parent data directory [./]
htmlpath=PATH : Path of parent html directory [./aa_ff]
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 []
badgenes=LIST : Genes to be moved to Lysate dataset []
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]
makepages=LIST : Types of pages to make [front,gene,nested,interactome,trees,complex]
titletext=FILE : File containing (Page,ID,Title) [titletext.tdt]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation. Based on rje_slimhtml.
    # 0.1 - Added Output for additional Pingu Analysis.
    # 0.2 - Added protein complex output.
    # 0.3 - Modified output for HAPPI analysis.