Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::Tools::TargetP - Results of one TargetP run


          use Bio::Tools::TargetP;

          #filename for  TargetP result :
          $targetp = Bio::Tools::TargetP->new(-file => 'targetp.out');

          # filehandle for TargetP :
          $targetp = Bio::Tools::TargetP->new( -fh  => \*INPUT );

          ### targetp v1.1 prediction results ##################################
          #Number of query sequences:  11
          #Cleavage site predictions included.
          #Using NON-PLANT networks.
          #Name                  Len            mTP     SP  other  Loc  RC  TPlen
          #swall|Q9LIP3|C72Y_AR  500          0.245  0.935  0.009   S    2     22
          #swall|Q52813|AAPQ_RH  400          0.170  0.462  0.577   _    5      -
          #swall|O86459|AAT_RHI  400          0.346  0.046  0.660   _    4      -

          # parse the results
          while($feature = $targetp->next_prediction()) {

                  #$feature is a Bio::SeqFeature::Generic object
                  my $method     = $targetp->analysis_method();
                  my $vesion     = $targetp->analysis_method_version() || $feature->source();
                  my $seqid      = $feature->seq_id();
                  # ...

          # essential if you gave a filename at initialization (otherwise the file
          # will stay open)


       TargetP modules will provides parsed information about protein localization.  It reads in
       a targetp output file.  It parses the results, and returns a Bio::SeqFeature::Generic
       object for each seqeunces found to have a subcellular localization


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AUTHORS - Emmanuel Quevillon


       Describe contact details here


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _


        Usage     : $self->analysis_method();
        Purpose   : Inherited method. Overridden to ensure that the name matches
        Returns   : String
        Argument  : n/a


         Title   : network
         Usage   : $self->network($network)
         Function: This method Get/Set the network used for the analysis (PLANT or NON-PLANT)
         Example :
         Returns : string
         Arguments: On set, the network used


         Title    :  cleavage
         Usage    : $self->cleavage($cleavage)
         Function : This method Get/Set if SignalP program was used to run TargetP
         Example  :
         Returns  : 1 or 0
         Arguments: On set, the cleavage used or not


         Usage    : $targetp->next_prediction()
         Purpose  : Returns the next TargetP prediction
         Returns  : A Bio::SeqFeature::Generic object
         Arguments: n/a


         Title     : create_feature
         Usage     : $self->create_feature(\%hash);
         Function  : This method creates a new Bio::SeqFeature::Generic object
         Example   :
         Returns   : Bio::SeqFeature::Generic
         Arguments : hash reference

        Title   : _initialize_state
        Usage   : n/a; usually called by _initialize() itself called by new()
        Function: This method is supposed to reset the state such that any 'history'
                  is lost. State information that does not change during object
                  lifetime is not considered as history, e.g. parent, name, etc shall
                  not be reset. An inheriting object should only be concerned with
                  state information it introduces itself, and for everything else
                  call SUPER::_initialize_state(@args).

                  The argument syntax is the same as for new() and _initialize(),
                  i.e., named parameters following the -name=>$value convention.
                  The following parameters are dealt with by the implementation
                  provided here:
                     -INPUT, -FH, -FILE
                  (tags are case-insensitive).
        Example :
        Returns :
        Args    :

         Usage    : $targetp->_prediction()
         Purpose  : Returns the number of TargetP predictions
         Returns  : A scalar (number)
         Arguments: n/a

        Title     : _parsed
        Usage     : $targetp->_parsed(1)
        Function  : This method is used to know if the output result is parsed or not
                    For internal use only
        Example   :
        Returns   : 1/0
        Arguments : 1/0 for setting

         Title    : _parse_results
         Usage    : $self->_parse_results()
         Function : This method parses a TargetP output
                    For internal use only
         Example  :
         Returns  : n/a
         Arguments: none

        Title    : _parse_line
        Usage    : $self->_parse_line($line)
        Function : This method parses the line result
                   For internal use only
        Example  :
        Returns  : Hash reference
        Arguemnts: line to parse

        Title    : _add_feature
        Usage    : $self->_add_feature($feature)
        Function : This method stores a feature object
                   For internal use only
        Example  :
        Returns  : n/a
        Arguments: Bio::SeqFeature::Generic

        Title    : _toString_location
        Usage    : $self->_toString_location($key)
        Function : This method convert the 'one letter code' location to
                   the corresponding definition
                   For internal use only
        Example  :
        Returns  : Location or undef
        Arguments: String