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Bob V0.5

Customised analysis module. Not for general consumption.

Module: Bob
Description: Customised analysis module. Not for general consumption.
Version: 0.5
Last Edit: 27/03/09

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


Imported modules: rje rje_db rje_slim rje_slimlist rje_zen


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

Function

This is the customised analysis pipeline for follow-up of my EnsDat Human SLiMFinder analysis. If this makes no sense to you, I don't think you want to be using this program, as it means that you are not me!

Commandline

GENERAL

motifs=FILE : File of motifs for selected analysis []
slimres=FILE : Name of SLiMFinder results file []
run=LIST : Analyses to run (pingu/feb/mar) []
generics=LIST : List of generic motifs for Pingu analysis []
knowns=FILE : File containing known SLiMs with columns "Pattern" & "Known"
runid=LIST : List of RunIDs to include in output (all if none) []

FEB

randres=FILE : File with results of random SLiMFinder runs. Will use for DS significance assessment. [None]
randfdr=PATH : Path to FDR files from random datasets []

MAR

resdir=PATH : Path to SLiMFinder results directory []
newres=FILE : Name for new results file [*.bob.csv]
remslim=LIST : List of SLiM Types to remove (varwild/krs) [varwild,krs]
recloud=T/F : Whether to try to recloud motifs once filtered [True]

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added "feb" method for Human SLiMFinder paper.
    # 0.2 - Added FDR calculations.
    # 0.3 - Added Random Results Ratio calculation as requested by Denis.
    # 0.4 - Added empirical random FDR.
    # 0.5 - Added filtering of motifs from results and regeneration of clouds before feb run. (mar run)

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