NAME

index_data.pl - Indexer and converter (ascii to binary) script for InterProScan datafiles.


SYNOPSIS

  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.


DESCRIPTION

  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)


VERSIONS

$Id: index_data.html,v 1.1.1.1 2005/08/18 13:18:26 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGMENTS

  Emmanuel Quevillon <tuco@ebi.ac.uk>