Seg - Seg utilities.
# examples here use Dispatcher::Tool::Seg;
$Id: Seg.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 Seg 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 Seg command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a seg result file and creates a hash table:
'nhits' => '2', '1' => { 'seqid' => 'swall|Q92455|ABF1_TRIRE', 'seqdesc' => 'Alpha-L-arabinofuranosidase precursor (EC 3.2.1.55) (Arabinosidase).', 'start' => '5', 'end' => '16' }, '2' => { 'seqid' => 'swall|Q92455|ABF1_TRIRE', 'seqdesc' => 'Alpha-L-arabinofuranosidase precursor (EC 3.2.1.55) (Arabinosidase).', 'start' => '369', 'end' => '384' }
Arguments: $href Reference to a hash. $result Path to a Seg 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