FingerPrintScan - FingerPrintScan utilities.
# examples here use Dispatcher::Tool::FingerPrintScan;
$Id: FingerPrintScan.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $
Copyright (c) European Bioinformatics Institute 2002
Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>
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
Description: Returns FingerPrintScan command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
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
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