NAME

FingerPrintScan - FingerPrintScan utilities.


SYNOPSIS

  # examples here
  use Dispatcher::Tool::FingerPrintScan;


DESCRIPTION


VERSIONS

$Id: FingerPrintScan.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 Description: Constructor allocates an anonymous hash, which
              is tied to the class.
 Arguments:   $name        FingerPrintScan tool name (optional). If given, sets
                           the Dispatcher::Config object automatically inside
                           the object. If not given, the Dispatcher::Config
                           must be set later with setConfig.
              $defaults    Default values for configuration, hash reference
                           (optional).
 Returns:     $self object

getCmdLine

 Description: Returns FingerPrintScan command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

 Description: Reads a fingerprintscan result file and creates a hash table:
              'seqname'  => 'WAP_RAT',
              'seqinfo'  => 'Fasta sequence',
              'besthit'  => { 'id'     => '4DISULPHCORE',
                              'evalue' => '3.528459e-08',
                              'desc'   => '4-disulphide core signature',
                              'pr'     => 'PR00003'
                            },
              'nhits'    => '4',
              'nmotifs'  => '10',
              'hits'     => { '1' => { 'id'        => '4DISULPHCORE',
                                       'nmotifs'   => '4  of  4',
                                       'sumid'     => '2e+02',
                                       'aveid'     => '49',
                                       'profscore' => '1112',
                                       'ppvalue'   => '4.4e-13',
                                       'evalue'    => '3.5e-08',
                                       'graphscan' => 'IIII' },
                              '2' => { ... },
                              ...
                            },
              'motifs'  => { '1' => { 'id'         => '4DISULPHCORE',
                                      'nmotifs'    => '1  of  4',
                                      'idscore'    => '46.67',
                                      'pfscore'    => '239',
                                      'pvalue'     => '9.35e-04',
                                      'sequence'   => 'EVQKAGRCPW',
                                      'len'        => '10',
                                      'low'        => '7',
                                      'pos'        => '76',
                                      'high'       => '1379' },
                             '2' => { ... },
                             ...
                           }
 Arguments:   $href          Reference to a hash.
              $result        Path to a FingerPrintScan result file.
 Returns:     1, ''  on success
              0, msg on failure

getRawResult

 Description: Returns raw formatted result string.
 Arguments:   $href      Reference to a result hash.
              $seqs      Sequence hash (see InterProScan::checkSequences).
              $iprscan   Reference to Dispatcher::Tool::InterProScan object.
                         Required for IPR fields and GO terms.
              $ipr       1: add IPR fields
                         0: no (default)
              $go        1: add GO terms
                         0: no (default)
 Returns:     1, str on success
              0, msg on failure