Bio::Tools
TargetP
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Summary
Bio::Tools::TargetP - Results of one TargetP run
Package variables
Privates (from "my" definitions)
$MAPLOC = { 'S' => 'Secretory pathway', 'M' => 'Mitochondrion', 'C' => 'Chloroplast', '_' => 'Any other', '*' => 'Unknown', '?' => 'Unknown', }
Included modules
Inherit
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
Methods
Methods description
Usage : $self->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
Returns : String
Argument : n/a |
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 |
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 |
Usage : $targetp->next_prediction()
Purpose : Returns the next TargetP prediction
Returns : A Bio::SeqFeature::Generic object
Arguments: n/a |
Title : create_feature
Usage : $self->create_feature(\%hash);
Function : This method creates a new Bio::SeqFeature::Generic object
Example :
Returns : Bio::SeqFeature::Generic
Arguments : hash reference |
Title : _initialize_state
Usage : n/a; usually called by _initialize() itself called by new()
Function: This method is supposed to reset the state such that any 'history'
is lost. State information that does not change during object
lifetime is not considered as history, e.g. parent, name, etc shall
not be reset. An inheriting object should only be concerned with
state information it introduces itself, and for everything else
call SUPER::_initialize_state(@args).
The argument syntax is the same as for new() and _initialize(),
i.e., named parameters following the -name=>$value convention.
The following parameters are dealt with by the implementation
provided here:
-INPUT, -FH, -FILE
(tags are case-insensitive).
Example :
Returns :
Args : |
Usage : $targetp->_prediction()
Purpose : Returns the number of TargetP predictions
Returns : A scalar (number)
Arguments: n/a |
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 |
Title : _parse_results
Usage : $self->_parse_results()
Function : This method parses a TargetP output
For internal use only
Example :
Returns : n/a
Arguments: none |
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 |
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 |
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 |
Methods code
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);} | sub network
{
my($self, $net) = @_;
if(defined($net)){
$self->{'_network'} = $net;
}
return $self->{'_network'};} | sub cleavage
{
my($self, $cleavage) = @_;
if(defined($cleavage)){
$self->{'_cleavage'} = $cleavage =~ /not included/ ? '0' : '1';
}
return $self->{'_cleavage'};} | sub next_prediction
{
my($self) = @_;
unless($self->_parsed()){
$self->_parse_results();
$self->_parsed(1);
}
return shift @{$self->{'_features'}} || undef;} | 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 => $self->analysis_method(),
-primary_tag => 'signal_peptide',
-strand => '+',
);
if(defined($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 $feature;} | sub _initialize_state
{
my ($self,@args,) = @_;
$self->SUPER::_initialize_state(@args);
$self->{'_features'} = [ ];
$self->{'_parameters'} = undef;
$self->{'_format'} = undef;
$self->{'_network'} = undef;
$self->{'_cleavage'} = undef;
$self->{'_parsed'} = 0;
$self->analysis_method('TargetP');
return 1; } | sub _predictions
{
my($self) = @_;
return scalar(@{$self->{'_features'}}) || 0;} | sub _parsed
{
my($self, $value) = @_;
if(defined($value)){
$self->{'_parsed'} = $value;
}
return $self->{'_parsed'};} | sub _parse_results
{
my($self) = @_;
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/){
$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;} | 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 $hash;} | sub _add_feature
{
my($self, $feature) = @_;
$self->throw("Need a Bio::SeqFeature::Generic object") unless $feature->isa("Bio::SeqFeature::Generic");
push(@{$self->{'_features'}}, $feature);
return;} | sub _toString_location
{
my($self, $key) = @_;
if($key && exists($MAPLOC->{$key})){
return $MAPLOC->{$key};
}
return;
}
1;} | General documentation
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
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.
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 | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _