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UniFake V1.3

Fake UniProt DAT File Generator

Program: UniFake
Description: Fake UniProt DAT File Generator
Version: 1.3
Last Edit: 17/04/12

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


Imported modules: rje rje_seq rje_tm rje_uniprot rje_zen


See SLiMSuite Blog for further documentation.

Function

This program runs a number of in silico predication programs and converts protein sequences into a fake UniProt DAT flat file. Additional features may be given as one or more tables, using the features=LIST option. Please see the UniFake Manual for more details.

Commandline

INPUT OPTIONS

seqin=FILE : Input sequence file. See rje_seq documentation for filtering options. [None]
spcode=X : Species code to use if it cannot be established from sequence name [None]
features=LIST : List of files of addtional features in delimited form []
aliases=FILE : File of aliases to be added to Accession number list (for indexing) [None]
pfam=FILE : PFam HMM download [None]
unipath=PATH : Path to real UniProt Datafile (will look here for DB Index file made with rje_dbase)
unireal=LIST : Real UniProt data to add to UniFake output ['AC','GN','RC','RX','CC','DR','PE','KW']
fudgeft=T/F : Fudge the real features left/right until a sequence match is found [True]

PROCESSING/OUTPUT OPTIONS

unifake=LIST : List of predictions to add to entries [tmhmm,signalp,disorder,pfam,uniprot]
datout=FILE : Name of output DAT file [Default input FILE.dat]
disdom=X : Disorder threshold below which to annotate PFam domain as "DOMAIN" [0.0]
makeindex=T/F : Whether to make a uniprot index file following run [False]
ensdat=T/F : Look for acc/pep/gene in sequence name [False]
tmhmm=FILE : Path to TMHMM program [None]
cleanup=T/F : Remove TMHMM files after run [True]
signalp=FILE : Path to SignalP program [None]

History Module Version History

    # 0.0 - Initial Compilation.
    # 1.0 - Version with full functionality.
    # 1.1 - Made changes to temp file names for parallel running
    # 1.2 - Added option for reading in Features and limited other info from real UniProt entry
    # 1.3 - Removed searching in UniProt if not UniReal features given.

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