Module: ORCFinder Description: Over-Represented Curation Finder Version: 0.0 Last Edit: 19/09/07

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_slimcore rje_zen

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

Function

This module is based on the SLiMFinder statistics for finding over-represented Short Linear Motifs. Instead of discovering motifs, however, ORCFinder reads in frequency data for UniProt features and analyses datasets for over- representation of these instead.

Commandline

### Basic Input/Output Options ###
ftlist=LIST : List of UniProt feature types to read in for analysis (default all features) []
ftfreq=FILE : File containing UPC frequencies of relevant feature subcategories [None]
seqin=FILE : Sequence file to search [None]
batch=LIST : List of files to search, wildcards allowed. (Over-ruled by seqin=FILE.) [*.dat,*.fas]
maxseq=X : Maximum number of sequences to process [500]
maxupc=X : Maximum UPC size of dataset to process [0]
walltime=X : Time in hours before program will abort search and exit [1.0]
resfile=FILE : Main SLiMFinder results table [slimfinder.csv]
resdir=PATH : Redirect individual output files to specified directory (and look for intermediates) [SLiMFinder/]
buildpath=PATH : Alternative path to look for existing intermediate files [SLiMFinder/]
force=T/F : Force re-running of BLAST, UPC generation and SLiMBuild [False]
pickup=T/F : Pick-up from aborted batch run by identifying last dataset output in resfile [False]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### Evolutionary Filtering ###
efilter=T/F : Whether to use evolutionary filter [True]
blastf=T/F : Use BLAST Complexity filter when determining relationships [True]
blaste=X : BLAST e-value threshold for determining relationships [1e=4]
altdis=FILE : Alternative all by all distance matrix for relationships [None]
gablamdis=FILE : Alternative GABLAM results file [None] (!!!Experimental feature!!!)
homcut=X : Max number of homologues to allow (to reduce large multi-domain families) [200]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### Special ###
makefreq=LIST : List of types of data for which to generate frequency data (makes ftfreq file) []

History Module Version History

    # 0.0 - Initial Compilation.