HMMPanther - Panther utilities.
# examples here use Dispatcher::Tool::HMMPanther;
$Id: HMMPanther.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $
Copyright (c) European Bioinformatics Institute 2002
Emmanuel Quevillon <tuco@ebi.ac.uk>
Description: Constructor allocates an anonymous hash, which is tied to the class. Arguments: $name HMMPanther 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 Hmmer command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a Hmmer result file and creates a hash table:
nhits => '2', '1' => { seqid => 'Y902_MYCTU', ndomains => '3', '1' => { methid => 'PF00672', desc => 'HAMP domain', start => '151', end => '219', score => '46.9', evalue => '4.3e-11' }, '2' => { methid => 'PF00512', desc => 'His Kinase A (phosphoacceptor) domain', start => '230', end => '296', score => '55.8', evalue => '9.2e-14' }, '3' => { methid => 'PF02518', desc => 'Histidine kinase-, DNA gyrase B-, and HSP90', start => '338', end => '445', score => '105.6', evalue => '9.6e-29' }, }, '2' => { seqid => 'WAP_RAT', ... }
Arguments: $href Reference to a hash. $result Path to a Hmmer result file. $inx Reference to a hash. 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