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
Bio::SeqFeature::Generic
Bio::Tools::AnalysisResult
Data::Dumper
Inherit
Bio::Tools::AnalysisResult
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
analysis_methodDescriptionCode
networkDescriptionCode
cleavageDescriptionCode
next_predictionDescriptionCode
create_featureDescriptionCode
_initialize_stateDescriptionCode
_predictionsDescriptionCode
_parsedDescriptionCode
_parse_resultsDescriptionCode
_parse_lineDescriptionCode
_add_featureDescriptionCode
_toString_locationDescriptionCode
Methods description
analysis_methodcode    nextTop
 Usage     : $self->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
Returns : String
Argument : n/a
networkcodeprevnextTop
  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
cleavagecodeprevnextTop
  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_predictioncodeprevnextTop
  Usage    : $targetp->next_prediction()
Purpose : Returns the next TargetP prediction
Returns : A Bio::SeqFeature::Generic object
Arguments: n/a
create_featurecodeprevnextTop
  Title     : create_feature
Usage : $self->create_feature(\%hash);
Function : This method creates a new Bio::SeqFeature::Generic object
Example :
Returns : Bio::SeqFeature::Generic
Arguments : hash reference
_initialize_statecodeprevnextTop
 Title   : _initialize_state
Usage : n/a; usually called by _initialize() itself called by new()
Function: This method is supposed to reset the state such that any 'history'
is lost. State information that does not change during object
lifetime is not considered as history, e.g. parent, name, etc shall
not be reset. An inheriting object should only be concerned with
state information it introduces itself, and for everything else
call SUPER::_initialize_state(@args).
The argument syntax is the same as for new() and _initialize(), i.e., named parameters following the -name=>$value convention. The following parameters are dealt with by the implementation provided here: -INPUT, -FH, -FILE (tags are case-insensitive). Example : Returns : Args :
_predictionscodeprevnextTop
  Usage    : $targetp->_prediction()
Purpose : Returns the number of TargetP predictions
Returns : A scalar (number)
Arguments: n/a
_parsedcodeprevnextTop
 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_resultscodeprevnextTop
  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_linecodeprevnextTop
 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_featurecodeprevnextTop
 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_locationcodeprevnextTop
 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
analysis_methoddescriptionprevnextTop
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);
}
networkdescriptionprevnextTop
sub network {
    my($self, $net) = @_;

    if(defined($net)){
	$self->{'_network'} = $net;
    }

    return $self->{'_network'};
}
cleavagedescriptionprevnextTop
sub cleavage {
    my($self, $cleavage) = @_;

    if(defined($cleavage)){
	$self->{'_cleavage'} = $cleavage =~ /not included/ ? '0' : '1';
    }

    return $self->{'_cleavage'};
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my($self) = @_;

    unless($self->_parsed()){
	$self->_parse_results();
	$self->_parsed(1);
    }

    return shift @{$self->{'_features'}} || undef;
}
create_featuredescriptionprevnextTop
sub create_feature {
    my($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 $feature;
}
_initialize_statedescriptionprevnextTop
sub _initialize_state {
  	my ($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; $self->analysis_method('TargetP'); return 1;
}
_predictionsdescriptionprevnextTop
sub _predictions {
    my($self) = @_;

    return scalar(@{$self->{'_features'}}) || 0;
}
_parseddescriptionprevnextTop
sub _parsed {
    my($self, $value) = @_;

    if(defined($value)){
	$self->{'_parsed'} = $value;
    }

    return $self->{'_parsed'};
}
_parse_resultsdescriptionprevnextTop
sub _parse_results {
    my($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;
}
_parse_linedescriptionprevnextTop
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 $hash;
}
_add_featuredescriptionprevnextTop
sub _add_feature {
    my($self, $feature) = @_;

    $self->throw("Need a Bio::SeqFeature::Generic object") unless $feature->isa("Bio::SeqFeature::Generic");

    push(@{$self->{'_features'}}, $feature);

    return;
}
_toString_locationdescriptionprevnextTop
sub _toString_location {
    my($self, $key) = @_;

    if($key && exists($MAPLOC->{$key})){
	return $MAPLOC->{$key};
    }

    return;
}



1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 QuevillonTop
Email emmanuel.quevillon@versailles.inra.fr
Describe contact details here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
PRIVATE METHODSTop