NAME

SignalP - SignalP utilities.


SYNOPSIS

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


DESCRIPTION


VERSIONS

$Id: SignalP.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        SignalP 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 SignalP command line.
 Arguments:   -
 Returns:     1, cmd on success
              0, msg on failure

parseResult

  Description: Reads a signalp result file and creates a hash table:
  Arguments:   $href          Reference to a hash.
               $result        Path to a SignalP result file.
               $inx           Reference to a hsah.
  Returns:     1, ''  on success
               0, msg on failure

_parseVersion1

  Description: Reads a signalp 1.x result file and creates a hash table:
              'nhits'   => '2',
              '1'       => { 'seqid'   => 'swall|Q9LIP3|C72Y_ARATH',
                             'seqdesc' => 'Cytochrome P450 71B37 (EC 1.14.-.-).',
                             '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 SignalP result file.
              $inx           Reference to a hash.
 Returns:     1, ''  on success
              0, msg on failure

_parseVersion2

 Description: Reads a signalp 2.0 output and creates a hash table.
              'nhits'   => '2',
              '1'       => { 'seqid'   => 'swall|Q9LIP3|C72Y_ARATH',
                             'seqdesc' => 'Cytochrome P450 71B37 (EC 1.14.-.-).',
                             '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 SignalP 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