index_data.pl - Indexer and converter (ascii to binary) script for InterProScan datafiles.
index_data.pl -f [file2index] -f [..] -inx [to index file] -iforce [force reindexing] -bin [to convert ascii datafile to binary] -bforce [force reconversion ascii to bin] -v [verbose(optional)] -h [display this help]
Options: -f The name of the file you want to index. See description below. -inx To tell the program you want to index one or several files. -iforce Force the reindex of the file if already indexed (update the index). -bin To tell the program to convert a hmm library file (ascii) to a binary file. This action will speed up the hmm analysis up to 40%. -bforce Force the reconversion of a ascii file to a binary if this file already exists. -v Be verbose during actions. -h Display a help and exit.
This script allow user to index or reindex (-iforce option) some files needed by InterProScan. You can give a list of files to be indexed. Supported files are : - interpro.xml - match.xml - smart.desc (not public) - smart.thresholds (not public) - superfamily.hmm - Pfam - Pfam-C - prints.pval - prodom.ipr - smart.HMMs - sf_hmm - TIGRFAMs_HMM.LIB - Gene3D.hmm
If the files are already indexed and up to date, the indexing is skipped unless you use -iforce option.
You can also use this script to convert or reconvert (-bforce) your ascii HMM datafile to binary file to speed up (~40%) the application using hmmer (Gene3D, Pfam, Tigr, Smart, PIR and Superfamily). Supported files for conversion are : - Pfam (Pfam) - TIGRFAMs_HMM.LIB (Tigr) - sf_hmm (PIR) - sf_hmm_sub (PIR) - smart.HMMs (Smart) - superfamily.hmm (Superfamily) - Gene3D.hmm (Gene3D)
Using the -bin option, the new binary file created will be named with a new extension '.bin' (e.g. Pfam -> Pfam.bin)
$Id: index_data.html,v 1.1.1.1 2005/08/18 13:18:26 hunter Exp $
Copyright (c) European Bioinformatics Institute 2002
Emmanuel Quevillon <tuco@ebi.ac.uk>