Bio::Tools Eponine
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Summary
Bio::Tools::Eponine - Results of one Eponine run
Package variables
No package variables defined.
Included modules
Bio::Tools::Prediction::Exon
Bio::Tools::Prediction::Gene
Inherit
Bio::Tools::AnalysisResult
Synopsis
 use Bio::Tools::Eponine;
use strict;
my $seq = "/data/seq.fa";
my $threshold = "0.999";
my @params = ( -seq => $seq,
-threshold => $threshold);
my $factory = Bio::Tools::Run::Eponine->new(@params); # run eponine against fasta my $r = $factory->run_eponine($seq); my $parser = Bio::Tools::Eponine->new($r); while (my $feat = $parser->next_prediction){ #$feat contains array of SeqFeature foreach my $orf($feat) { print $orf->seq_id. "\n"; } }
Description
Parser for Eponine, a probabilistic transcription start site detector
optimized for mammalian genomic sequence. This module inherits off
Bio::Tools::AnalysisResult and therefore implements
Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and
Bio::SeqAnalysisParserI).
Methods
_initialize_state
No description
Code
analysis_methodDescriptionCode
next_featureDescriptionCode
next_predictionDescriptionCode
_parse_predictionsDescriptionCode
create_featureDescriptionCode
_predictionDescriptionCode
_predictions_parsedDescriptionCode
Methods description
analysis_methodcode    nextTop
 Usage     : $mzef->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/mzef/i.
Returns : String
Argument : n/a
next_featurecodeprevnextTop
 Title   : next_feature
Usage : while($gene = $mzef->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object. This method is required for classes implementing the SeqAnalysisParserI interface, and is merely an alias for next_prediction() at present. Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
next_predictioncodeprevnextTop
 Title   : next_prediction
Usage : while($gene = $mzef->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
Note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes but just potential internal exons. Example : Returns : A Bio::Tools::Prediction::Gene object. Args :
_parse_predictionscodeprevnextTop
 Title   : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
create_featurecodeprevnextTop
    Title   :   create_feature
Usage : obj->create_feature($feature)
Function: Returns an array of features
Returns : Returns an array of features
Args : none
_predictioncodeprevnextTop
 Title   : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
Methods code
_initialize_statedescriptionprevnextTop
sub _initialize_state {
    my($self,@args) = @_;

    # first call the inherited method!
my $make = $self->SUPER::_initialize_state(@args); # handle our own parameters
# our private state variables
$self->{'_preds_parsed'} = 0; #array of Bio::SeqFeatures
$self->{'_flist'} =[];
}
analysis_methoddescriptionprevnextTop
sub analysis_method {
 #-------------
my ($self, $method) = @_; if($method && ($method !~ /epo/i)) { $self->throw("method $method not supported in " . ref($self)); } return $self->SUPER::analysis_method($method);
}
next_featuredescriptionprevnextTop
sub next_feature {
    my ($self,@args) = @_;
    # even though next_prediction doesn't expect any args (and this method
# does neither), we pass on args in order to be prepared if this changes
# ever
return $self->next_prediction(@args);
}
next_predictiondescriptionprevnextTop
sub next_prediction {
    my ($self) = @_;
    my $gene;

    # if the prediction section hasn't been parsed yet, we do this now
$self->_parse_predictions() unless $self->_predictions_parsed(); # return the next gene structure (transcript)
return $self->_prediction();
}
_parse_predictionsdescriptionprevnextTop
sub _parse_predictions {
    my ($self) = @_;

    while(defined($_ = $self->_readline())) {
        if (! /^\#/){ #ignore introductory lines
my @element = split; my (%feature); $feature {name} = $element[0]; $feature {score} = $element[5]; $feature {start} = $element[3]; $feature {end} = $element[4]; $feature {strand} = $element[6]; $feature {source}= 'Eponine'; $feature {primary}= 'TSS'; $feature {program} = 'eponine-scan'; $feature {program_version} = '2'; $self->create_feature(\%feature); next; } } $self->_predictions_parsed(1);
}
create_featuredescriptionprevnextTop
sub create_feature {
    my ($self, $feat) = @_;
     #create and fill Bio::EnsEMBL::Seqfeature object
my $tss = Bio::SeqFeature::Generic->new ( -seq_id => $feat->{'name'}, -start => $feat->{'start'}, -end => $feat->{'end'}, -strand => $feat->{'strand'}, -score => $feat->{'score'}, -source_tag => $feat->{'source'}, -primary_tag => $feat->{'primary'}); if ($tss) { # add to _flist
push(@{$self->{'_flist'}}, $tss); } #print $tss->gff_string;
}
_predictiondescriptionprevnextTop
sub _prediction {
    my ($self) = @_;

    return unless(exists($self->{'_flist'}) && @{$self->{'_flist'}});
    return shift(@{$self->{'_flist'}});
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    # array of pre-parsed predictions
if(! exists($self->{'_preds_parsed'})) { $self->{'_preds_parsed'} = 0; } return $self->{'_preds_parsed'}; } 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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Tania Oh Top
<gisoht-at-nus.edu.sg>
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _