BlastProDom - BlastProDom utilities.
# examples here use Dispatcher::Tool::BlastProDom;
$Id: BlastProDom.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 BlastProDom 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 BlastProDom command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a blastprodom result file and creates a hash table:
'nhits' => '5' '1' => { 'seqid' => 'USERPROTEIN:tmp_job3' 'start' => '2', 'end' => '7', 'methid' => 'pd_PD383194', 'sp' => 'sp_Q9X2E3_THEMA_Q9X2E3', 'dstart' => '129' 'dend' => '280' 'score' => '81', 'evalue' => '3e-09', 'desc' => '(22) PROTEOME COMPLETE PROTEASE HFLC HYDROLASE 3.4.-.- SERINE TRANSMEMBRANE FOR FTSH', 'length' => '152' }, '2' = { ... } ...
Arguments: $href Reference to a hash. $result Path to a BlastProDom 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