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rje_pattern_discovery V1.3

Pattern Discovery Module

Module: rje_pattern_discovery
Description: Pattern Discovery Module
Version: 1.3
Last Edit: 07/10/06

Copyright © 2006 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_seq


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

Function

Calls and tidies TEIRESIAS. Will add SLIMDISC in time. Will also read motifs and output information content.

SLiMDisc Searching (Tested with slimdisc_V1.3.py)

seqin=FILE : Sequence File to search [None]
slimfiles=LIST : List of files for SLiMDisc discovery. May have wildcards. (Over-ruled by seqin=FILE.) [*.fas]
minsup=X : Min. number of sequences to have in file [3]
maxsup=X : Max. number of sequences to have in file [0]
slimdisc=T/F : Whether to run list of files through SLiMDisc [False]
slimopt="X" : Text string of additional SLiMDisc options [""]
useres=T/F : Whether to use existing results files or overwrite (-BT -TT) [True]
remhub=X : If X > 0.0, removes "hub" protien ("HUB_PPI") and any proteins >=X% identity to hub [0.0]
: Renames datasets as -RemHub, -KeptHub or -NoHub
slimsupport=X : Min. SLiMDisc support (-S X). If < 1, it is a proportion of input dataset size. [0.1]
slimranks=X : Return top X SLiMDisc ranked sequences [1000]
slimwall=X : TEIRESIAS walltime (minutes) in SLiMDisc run (-W X) [60]
slimquery=T/F : Whether to pull out Query Protein from name of file qry_QUERY [False]
memsaver=T/F : Whether to run SLiMDisc in memory_saver mode (-X T) [True]
bigfirst=T/F : Whether to run the biggest datasets first (e.g. for ICHEC taskfarm) [True]
slimversion=X : Version of SLiMDisc to run (See slimcall=X for batch file jobs) [1.4]

Batch File Output options

batchout=FILE : Create a batch file containing individual seqin=FILE calls. [None]
slimcall="X" : Call for SLiMDisc in batch mode. May have leading commands. ["python slimdisc_V1.4.py"]

TEIRESIAS Searching

mysql=T/F : MySQL mode [True]
delimit=X : Text delimiter [\\t]
info=FILE : Calculate information content of motifs in FILE (based on AA Freq from seqin, if given) [None]
igap=X : Information Content "Gap penalty" (wildcard penalisation) [0]
outfile=FILE : Output file name [seqin.teiresias.*]
teiresias=T/F : Whether to perform TEIRESIAS search on seqin=FILE [True]
teiresiaspath=PATH : Path to TEIRESIAS ['c:/bioware/Teiresias/teiresias_char.exe'] * Use forward slashes (/)
teiresiasopt=X : Options for TEIRESIAS Search (Remember "X Y Z" for spaced cmds) e.g. "-bc:\bioware\Teiresias\equiv.txt"
["-l3 -w10 -c1 -k2 -p"]


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