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

NAME

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

SYNOPSIS

          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->close();

DESCRIPTION

       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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHORS - Emmanuel Quevillon

       Email emmanuel.quevillon@versailles.inra.fr

       Describe contact details here

APPENDIX

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

analysis_method

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

network

         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

cleavage

         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

next_prediction

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

create_feature

         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

   PRIVATE METHODS
   _initialize_state
        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    :

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

   _parsed
        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

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

   _parse_line
        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

   _add_feature
        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

   _toString_location
        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