NAME

HMMPIR - HMMPIR utilities.


SYNOPSIS

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


DESCRIPTION


VERSIONS

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

Copyright (c) European Bioinformatics Institute 2002


AUTHORS / ACKNOWLEDGEMENTS

Ville Silventoinen <vsi@ebi.ac.uk> Emmanuel Quevillon <tuco@ebi.ac.uk>

new

 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

getCmdLine

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

parseResult

 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

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