NAME

HMMPanther - Panther utilities.


SYNOPSIS

  # examples here
  use Dispatcher::Tool::HMMPanther;


DESCRIPTION


VERSIONS

$Id: HMMPanther.pm.html,v 1.1.1.1 2005/08/18 13:18:25 hunter Exp $

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 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

getCmdLine

 Description: Returns Hmmer command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

 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

getRawResult

 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