HMMPIR - HMMPIR utilities.
# examples here use Dispatcher::Tool::HMMPIR;
$Id: HMMPIR.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 HMMPIR 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 HMMPIR command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a HMMPIR result file and creates a hash table:
nhits => '2', '1' => { 'seqid' => 'NF00181542', 'methid' => 'PIRSF001424', 'pirdesc' => 'Prephenate dehydratase', 'start' => '1', 'end' => '270', 'score' => '474.8', 'evalue' => '6e-142' }, '2' => { 'seqid' => 'NF00181707', 'methid' => 'PIRSF006414', 'pirdesc' => 'Formylmethanofuran--tetrahydromethanopterin formyltransferase', 'start' => '1', 'end' => '301', 'score' => '772.3', 'evalue' => '1.7e-231' }
Arguments: $href Reference to a hash. $result Path to a HMMPIR 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