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Bio::Tools::TargetP(3)User Contributed Perl DocumentatioBio::Tools::TargetP(3)

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

perl v5.24.1			  2017-07-08		Bio::Tools::TargetP(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Emmanuel Quevillon | APPENDIX | analysis_method | network | cleavage | next_prediction | create_feature

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