#
# Bioperl module for TargetP
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Emmanuel Quevillon <emmanuel.quevillon@versailles.inra.fr>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::TargetP - Results of one TargetP run
=head1 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();
=head1 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
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
=head1 AUTHORS - Emmanuel Quevillon
Email emmanuel.quevillon@versailles.inra.fr
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::TargetP;
use strict;
use Bio::Tools::AnalysisResult;
use Bio::SeqFeature::Generic;
use Data::Dumper;
use base qw(Bio::Tools::AnalysisResult);
#Definition of 'Loc' field according to http://www.cbs.dtu.dk/services/TargetP/output.php
my $MAPLOC = {
'S' => 'Secretory pathway',
'M' => 'Mitochondrion',
'C' => 'Chloroplast',
'_' => 'Any other',
'*' => 'Unknown',
'?' => 'Unknown',
};
=head1 analysis_method
Usage : $self->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
Returns : String
Argument : n/a
=cut
sub analysis_method {
my ($self, $method) = @_;
if($method && ($method !~ /TargetP/i)) {
$self->throw("method $method not supported in " . ref($self));
}
return $self->SUPER::analysis_method($method);
}
=head1 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
=cut
sub network {
my($self, $net) = @_;
if(defined($net)){
$self->{'_network'} = $net;
}
return $self->{'_network'};
}
=head1 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
=cut
sub cleavage {
my($self, $cleavage) = @_;
if(defined($cleavage)){
$self->{'_cleavage'} = $cleavage =~ /not included/ ? '0' : '1';
}
return $self->{'_cleavage'};
}
=head1 next_prediction
Usage : $targetp->next_prediction()
Purpose : Returns the next TargetP prediction
Returns : A Bio::SeqFeature::Generic object
Arguments: n/a
=cut
sub next_prediction {
my($self) = @_;
unless($self->_parsed()){
$self->_parse_results();
$self->_parsed(1);
}
return shift @{$self->{'_features'}} || undef;
}
=head1 create_feature
Title : create_feature
Usage : $self->create_feature(\%hash);
Function : This method creates a new Bio::SeqFeature::Generic object
Example :
Returns : Bio::SeqFeature::Generic
Arguments : hash reference
=cut
sub create_feature {
my($self, $feat) = @_;
$self->throw("Need a reference to hash table") unless($feat && ref($feat) eq 'HASH');
my $feature = Bio::SeqFeature::Generic->new(
-seq_id => $feat->{seqid},
-source_tag => $self->analysis_method(),
-primary_tag => 'signal_peptide', #Sequence Ontology compliant
-strand => '+',
);
if(defined($feat->{seqlen})){
$feature->start(1);
$feature->end($feat->{seqlen});
}
$feature->add_tag_value('location', $MAPLOC->{$feat->{loc}}) if(exists($MAPLOC->{$feat->{loc}}));
$feature->add_tag_value('chloroplastCutOff', $feat->{cTP}) if(defined($feat->{cTP}));
$feature->add_tag_value('mitochondrionCutOff', $feat->{mTP}) if(defined($feat->{mTP}));
$feature->add_tag_value('signalPeptideCutOff', $feat->{SP}) if(defined($feat->{SP}));
$feature->add_tag_value('otherCutOff', $feat->{other}) if(defined($feat->{other}));
$feature->add_tag_value('reliabilityClass', $feat->{RC}) if(defined($feat->{RC}));
$feature->add_tag_value('signalPeptideLength', $feat->{TPLen}) if(defined($feat->{TPLen}));
$feature->add_tag_value('network', $self->network());
return $feature;
}
=head2 PRIVATE METHODS
=cut
=head2 _initialize_state
Title : _initialize_state
Usage : n/a; usually called by _initialize() itself called by new()
Function: This method is supposed to reset the state such that any 'history'
is lost. State information that does not change during object
lifetime is not considered as history, e.g. parent, name, etc shall
not be reset. An inheriting object should only be concerned with
state information it introduces itself, and for everything else
call SUPER::_initialize_state(@args).
The argument syntax is the same as for new() and _initialize(),
i.e., named parameters following the -name=>$value convention.
The following parameters are dealt with by the implementation
provided here:
-INPUT, -FH, -FILE
(tags are case-insensitive).
Example :
Returns :
Args :
=cut
sub _initialize_state {
my ($self,@args,) = @_;
# first call the inherited method!
$self->SUPER::_initialize_state(@args);
# our private state variables
$self->{'_features'} = [ ];
$self->{'_parameters'} = undef;
$self->{'_format'} = undef;
$self->{'_network'} = undef;
$self->{'_cleavage'} = undef;
$self->{'_parsed'} = 0;
$self->analysis_method('TargetP');
return 1;
}
=head2 _predictions
Usage : $targetp->_prediction()
Purpose : Returns the number of TargetP predictions
Returns : A scalar (number)
Arguments: n/a
=cut
sub _predictions {
my($self) = @_;
return scalar(@{$self->{'_features'}}) || 0;
}
=head2 _parsed
Title : _parsed
Usage : $targetp->_parsed(1)
Function : This method is used to know if the output result is parsed or not
For internal use only
Example :
Returns : 1/0
Arguments : 1/0 for setting
=cut
sub _parsed {
my($self, $value) = @_;
if(defined($value)){
$self->{'_parsed'} = $value;
}
return $self->{'_parsed'};
}
=head2 _parse_results
Title : _parse_results
Usage : $self->_parse_results()
Function : This method parses a TargetP output
For internal use only
Example :
Returns : n/a
Arguments: none
=cut
sub _parse_results {
my($self) = @_;
### 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 -
while(defined(my $line = $self->_readline())){
if($line =~ /targetp (v[\d\.]+)/){
$self->analysis_method_version($1);
}elsif($line =~ /Cleavage site predictions (.*)/){
$self->cleavage($1);
}elsif($line =~ /Using (\S+) networks/){
$self->network($1);
}elsif($line =~ /^Name/){
#We skip the next line which is '------------------'
$self->_readline();
my $hash = { };
while(defined(my $line = $self->_readline())){
last if($line =~ /^----/);
my $hash = $self->_parse_line($line);
my $new_feature = $self->create_feature($hash);
$self->_add_feature($new_feature);
}
}
}
return;
}
=head2 _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
=cut
sub _parse_line {
my($self, $line) = @_;
$self->throw("No line to parse given") unless($line);
my $hash = { };
my ($seqid, $seqlen, $cTP, $mTP, $SP, $other, $loc, $RC, $TPlen);
if($self->network() eq 'NON-PLANT'){
($seqid, $seqlen, $mTP, $SP, $other, $loc, $RC, $TPlen) = split(/\s+/, $line);
}else{
($seqid, $seqlen, $cTP, $mTP, $SP, $other, $loc, $RC, $TPlen) = split(/\s+/, $line);
}
$hash->{seqid} = $seqid;
$hash->{seqlen} = $seqlen;
$hash->{cTP} = $cTP || undef;
$hash->{mTP} = $mTP;
$hash->{SP} = $SP;
$hash->{other} = $other;
$hash->{loc} = $loc;
$hash->{RC} = $RC;
$hash->{TPLen} = ($TPlen && $TPlen =~ /\d+/) ? $TPlen : undef;
return $hash;
}
=head2 _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
=cut
sub _add_feature {
my($self, $feature) = @_;
$self->throw("Need a Bio::SeqFeature::Generic object") unless $feature->isa("Bio::SeqFeature::Generic");
push(@{$self->{'_features'}}, $feature);
return;
}
=head2 _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
=cut
sub _toString_location {
my($self, $key) = @_;
if($key && exists($MAPLOC->{$key})){
return $MAPLOC->{$key};
}
return;
}
1;