Christopher Fields > BioPerl-1.6.921 > Bio::Tools::TargetP

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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924

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://redmine.open-bio.org/projects/bioperl/

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
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