ProfileScan - ProfileScan utilities.
# examples here use Dispatcher::Tool::ProfileScan;
$Id: ProfileScan.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 ProfileScan 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 ProfileScan command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a profilescan result file and creates a hash table:
'nhits' => '2' '1' => { 'seqid' => 'WAP_RAT', 'hitid' => 'CYS_RICH', 'evalue' => '9.927', 'pos' => '41', 'start' => '45', 'end' => '123', 'methid' => 'PS50311', 'psdesc' => 'CYS_RICH Cysteine-rich region.' }, '2' => { ... }
Arguments: $href Reference to a hash. $result Path to a ProfileScan 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