Raw content of Bio::Das::ProServer::SourceAdaptor::efg_result_set
<![CDATA[=head1 NAME
efg_feature_set.pm
=head1 SYNOPSIS
Proserver module to run DAS server off the efg FeatureSet table
=head1 DESCRIPTION
=head1 LICENCE
This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.
=head1 AUTHOR
Stefan Graf <graef@ebi.ac.uk>, Ensembl Functional Genomics
=head1 CONTACT
Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>
=cut
package Bio::Das::ProServer::SourceAdaptor::efg_result_set;
use warnings;
use strict;
use Data::Dumper;
use IO::File;
use base qw(Bio::Das::ProServer::SourceAdaptor);
sub init
{
my ($self) = @_;
$self->{'capabilities'} = {
'features' => '1.0',
'stylesheet' => '1.0'
};
}
sub title {
my $self = shift;
my ($title) = $self->dsn;
$title =~ s/\./_/;
return "$title";
}
sub build_features
{
my ( $self, $args ) = @_;
#print Dumper $args;
my $segment = $args->{'segment'} || return ();
my $start = $args->{'start'} || return ();
my $end = $args->{'end'} || return ();
my $dba = $self->transport->adaptor();
my $slice = $dba->get_SliceAdaptor->fetch_by_region
('chromosome', $segment, $start, $end);
print Dumper $slice if ($self->{'debug'});
my $rset = $dba->get_ResultSetAdaptor->fetch_by_dbID
($self->config()->{'result_set_id'});
my @features;
map {
my $ft_start = $start+$_->start();
my $ft_end = $start+$_->end();
my $id = sprintf( "%s:%s,%s",
$segment,
$ft_start,
$ft_end);
#print Dumper $id if ($self->{'debug'});
push @features, {
'id' => $id,
'label' => $id,
'start' => $ft_start,
'end' => $ft_end,
#'ori' => 1,
'score' => $_->score,
'method' => $self->config()->{'source'},
'type' => $self->config()->{'type'},
'typecategory'=> $self->config()->{'category'},
#'note' => $note,
#'link' => 'http://www.sanger.ac.uk/PostGenomics/epigenome/',
#'linktxt' => 'Human Epigenome Project (HEP)'
}
} @{$rset->get_ResultFeatures_by_Slice($slice)};
# # get data via straight SQL
# my $version = $self->config()->{'data_version'};
# my $result_set_id = $self->config()->{'result_set_id'};
# my $qbounds = ($start && $end)?
# qq( AND pf.seq_region_start<=$end AND pf.seq_region_end>=$start):"";
#
# my $sql = "SELECT STRAIGHT_JOIN pf.seq_region_start as start, pf.seq_region_end as end,
# pf.seq_region_strand as strand, r.score as score
# FROM probe_feature pf, result r, chip_channel cc, seq_region sr
# WHERE cc.result_set_id = $result_set_id
# AND cc.chip_channel_id = r.chip_channel_id
# AND r.probe_id = pf.probe_id
# AND sr.seq_region_id=pf.seq_region_id
# AND sr.schema_build=\"$version\"
# AND sr.name=\"$segment\"".
# $qbounds.";";
#
# print Dumper $sql if ($self->{'debug'});
#
# my $features = $self->transport->query($sql);
# print Dumper $features if ($self->{'debug'});
#
# my @features;
#
# map {
# my $id = sprintf( "%s:%d,%d",
# $segment,
# $_->{'start'},
# $_->{'end'});
# #print Dumper $id if ($self->{'debug'});
# push @features, {
#
# 'id' => $id,
# 'label' => $id,
# 'start' => $_->{'start'},
# 'end' => $_->{'end'},
# #'ori' => 1,
# 'score' => $_->{'score'},
# 'method' => $self->config()->{'source'},
# 'type' => $self->config()->{'type'},
# 'typecategory'=> $self->config()->{'category'},
# #'note' => $note,
# #'link' => 'http://www.sanger.ac.uk/PostGenomics/epigenome/',
# #'linktxt' => 'Human Epigenome Project (HEP)'
#
# }
#
# } @{$features};
print 'NoRF: '.scalar(@features)."\n";
return @features;
# my $dset = $dba->get_DataSetAdaptor->fetch_by_dbID
# ($self->config()->{'data_set_id'});
# #print Dumper $dset->get_supporting_sets;
#
# my @features;
#
# foreach my $rset (@{$dset->get_supporting_sets()})
# {
#
# #print Dumper $rset->get_ResultFeatures_by_Slice($slice);
# map {
# #print Dumper $_;
# my $ft_start = $start+$_->start;
# my $ft_end = $start+$_->end;
# my $id = sprintf( "%s:%s,%s",
# $segment,
# $ft_start,
# $ft_end);
# #print Dumper $id;
# push @features, {
#
# 'id' => $id,
# 'label' => $id,
# 'start' => $ft_start,
# 'end' => $ft_end,
# #'ori' => 1,
# 'score' => $_->score,
# 'method' => $self->config()->{'source'},
# 'type' => $self->config()->{'type'},
# 'typecategory'=> $self->config()->{'category'},
# #'note' => $note,
# #'link' => 'http://www.sanger.ac.uk/PostGenomics/epigenome/',
# #'linktxt' => 'Human Epigenome Project (HEP)'
#
# } } @{$rset->get_ResultFeatures_by_Slice($slice)};
#
# return @features;
#
# }
# my $type = $self->config()->{'type'};
# my $feature_set_id = $self->config()->{'feature_set_id'};
# print Dumper $feature_set_id if ($self->{'debug'});
#
# # get data
#
# my $qbounds = ($start && $end)?qq(AND seq_region_start <= $end AND seq_region_end >= $start):"";
# my $version = $self->config()->{'version'};
# my $sql = "SELECT *
# FROM ${type}_feature f, seq_region sr
# WHERE sr.seq_region_id=f.seq_region_id
# AND sr.name=\"$segment\"
# AND sr.schema_build=\"$version\"
# AND f.feature_set_id=$feature_set_id
# $qbounds";
#
# print Dumper $sql if ($self->{'debug'});
#
# my $features = $self->transport->query($sql);
#
# print Dumper $features if ($self->{'debug'});
# #print "Number of features: ", scalar(@{$features}), "\n";
#
# foreach my $ft (@{$features}) {
#
# my $id = sprintf( "%s:%s,%s",
# $segment,
# $ft->{'seq_region_start'},
# $ft->{'seq_region_end'}
# );
#
# my $note = $ft->{'display_label'};
#
# push @features,
# {
# 'id' => $id,
# 'label' => $id,
# 'start' => $ft->{'seq_region_start'},
# 'end' => $ft->{'seq_region_end'},
# 'ori' => $ft->{'seq_region_strand'},
# 'score' => $ft->{'score'},
## #'method' => $self->config()->{'source'},
# 'type' => $type,
## #'typecategory'=> $self->config()->{'category'},
# 'note' => $note,
## 'link' => 'http://www.sanger.ac.uk/PostGenomics/epigenome/',
## 'linktxt' => 'Human Epigenome Project (HEP)'
# };
# }
#
}
sub das_stylesheet
{
my $self = shift;
return <<EOT;
<!DOCTYPE DASSTYLE SYSTEM "http://www.biodas.org/dtd/dasstyle.dtd">
<DASSTYLE>
<STYLESHEET version="0.01">
<CATEGORY id="default">
<TYPE id="default">
<GLYPH>
<TILING>
<HEIGHT>30</HEIGHT>
<COLOR1>brown3</COLOR1>
</TILING>
</GLYPH>
</TYPE>
</CATEGORY>
</STYLESHEET>
</DASSTYLE>
EOT
}
1;
]]>