Module: SLiMFRAP Description: SLiMFinder Results Analysis Pipeline Version: 0.1 Last Edit: 06/10/09

Copyright © 2009 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_genemap rje_go rje_slim rje_zen slimjim comparimotif_V3

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

Function

Customised analysis pipeline for High Throughput SLiMFinder runs.

Commandline

INPUT OPTIONS

resfiles=LIST : List of results files to read in and process []
resdir=PATH : Path to extra SLiMFinder results files (*.occ.csv) []
pairwise=FILE : Pingu Pairwise PPI file [None]
elm=FILE : File of ELM Motifs [None]
nandr=FILE : File of Neduva & Russell motifs [None]
pickledata=FILE : Genemap pickle to import and use. (See other rje_genemap options) [None]
domtable=FILE : Table of domain predictions [None]
direct=LIST : Evidence codes for direct interactions []
indirect=LIST : Evidence codes for indirect interactions []
usego=T/F : Whether to use GO datasets [False]
usenandr=T/F : Whether to use Neduva & Russell results [False]

PROCESSING OPTIONS

generics=LIST : List of pattern annotation to screen as generic motifs []
knowns=FILE : File containing known SLiMs with columns "Pattern" & "Known"
tp=FILE : File containing known SLiMs with columns "Known", "Hub" & "Type"
annotate=T/F : Whether to manually annotate/classify SLiMs [False]
skipknown=T/F : Whether to skip known SLiMs in manual annotation (True), or ask to check (False) [False]
skipann=LIST : List of auto-annotations to skip from manual annotation [rand]
screenelm=LIST : List of ELMs to screen from CompariMotif [LIG_Sin3_3,TRG_NES_1]
fdranncut=X : FDR cut-off for manual annotation [0.05]
slimjim=T/F : Whether to process data for SLiMJIM output [True]

OUTPUT OPTIONS

frapout=T/F : Whether to generate SLiMFRAP 0.0 output tables [False]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added SLiMJIM output.