TMHMM - TMHMM utilities.
# examples here use Dispatcher::Tool::TMHMM;
$Id: TMHMM.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 TMHMM 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 TMHMM command line. Arguments: - Returns: 1, cmd on success 0, msg on failure
Description: Reads a tmhmm 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' => '1', 'end' => '23' }, '2' => { 'seqid' => 'swall|Q9LIP4|C72X_ARATH', 'seqdesc' => 'Cytochrome P450 71B36 (EC 1.14.-.-).', 'start' => '1', 'end' => '19' }
Arguments: $href Reference to a hash. $result Path to a TMHMM result file. Returns: 1, '' on success 0, msg on failure
Description: Returns raw formatted result string. Arguments: $href Reference to a result hash. $seqid Sequence ID. $seqcrc CRC64 checksum. $seqlen Sequence length. $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