Raw content of Bio::Tools::Eponine
<![CDATA[# $Id: Eponine.pm,v 1.7 2002/10/22 07:38:45 lapp Exp $
#
# BioPerl module for Bio::Tools::Eponine
#
# Cared for by Tania Oh <gisoht@nus.edu.sg>
#
# Copyright Tania Oh
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Eponine - Results of one Eponine run
=head1 SYNOPSIS
use Bio::Tools::Run::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 $orf->seq_id. "\n";
}
}
=head1 DESCRIPTION
Parser for Eponine, a probabilistic transcription start site detector
optimized for mammalian genomic sequence. This module inherits off
Bio::Tools::AnalysisResult and therefore implements
Bio::SeqAnalysisParserI (see L<Bio::Tools::AnalysisResult> and
L<Bio::SeqAnalysisParserI>).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Tania Oh
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Eponine;
use vars qw(@ISA);
use strict;
use Bio::Tools::AnalysisResult;
use Bio::Tools::Prediction::Gene;
use Bio::Tools::Prediction::Exon;
@ISA = qw(Bio::Tools::AnalysisResult);
sub _initialize_state {
my($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'} =[];
}
=head2 analysis_method
Usage : $mzef->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/mzef/i.
Returns : String
Argument : n/a
=cut
#-------------
sub analysis_method {
#-------------
my ($self, $method) = @_;
if($method && ($method !~ /epo/i)) {
$self->throw("method $method not supported in " . ref($self));
}
return $self->SUPER::analysis_method($method);
}
=head2 next_feature
Title : next_feature
Usage : while($gene = $mzef->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Note that with the present version of MZEF there will only be one
object returned, because MZEF does not predict individual genes
but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_feature {
my ($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 $self->next_prediction(@args);
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $mzef->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
Note that with the present version of MZEF there will only be one
object returned, because MZEF does not predict individual genes
but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
=cut
sub next_prediction {
my ($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();
}
=head2 _parse_predictions
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
=cut
sub _parse_predictions {
my ($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;
}
}
$self->_predictions_parsed(1);
}
=head2 create_feature
Title : create_feature
Usage : obj->create_feature($feature)
Function: Returns an array of features
Returns : Returns an array of features
Args : none
=cut
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;
}
=head2 _prediction
Title : _prediction()
Usage : $gene = $obj->_prediction()
Function: internal
Example :
Returns :
=cut
sub _prediction {
my ($self) = @_;
return undef unless(exists($self->{'_flist'}) && @{$self->{'_flist'}});
return shift(@{$self->{'_flist'}});
}
=head2 _predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
=cut
sub _predictions_parsed {
my ($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;
]]>