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 AT bioperl DOT 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 AT bioperl DOT 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 DOT quevillon AT versailles DOT inra DOT 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