/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::TargetP

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