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Bio::Tools::TargetP.3pm

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 informations 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:

   http://bugzilla.open-bio.org/
 
 

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