Raw content of BioMart::Formatter::HTML_36
<![CDATA[# $Id: HTML_36.pm,v 1.1 2007/10/19 13:20:22 w3adm Exp $
#
# BioMart module for BioMart::Formatter::HTML_36
#
# You may distribute this module under the same terms as perl
# itself.
# POD documentation - main docs before the code.
=head1 NAME
BioMart::Formatter::HTML_36
=head1 SYNOPSIS
The HTML_36 Formatter returns data formatted into a HTML_36 table
for a BioMart query's ResultTable
=head1 DESCRIPTION
When given a BioMart::ResultTable containing the results of
a BioMart::Query the HTML_36 Formatter will return HTML_36 formatted tabular
output. The getDisplayNames and getFooterText can be used to return
appropiately formatted headers and footers respectively. If hyperlink
templates are defined for the attributes in the Dataset's ConfigurationTree
then appropiate hyperlinks will be calculated for each cell of the table.
Addition of any extra attributes to the Query that may be required for this
hyperlink formatting is handled in this Formatter
=head1 AUTHORS
=over
=item *
Damian Smedley
=item *
Gudmundur Thorisson
=back
=head1 CONTACT
This module is part of the BioMart project
http://www.biomart.org
Questions can be posted to the mart-dev mailing list:
mart-dev@ebi.ac.uk
=head1 METHODS
=cut
package BioMart::Formatter::HTML_36;
use strict;
use warnings;
use Readonly;
use EnsEMBL::Web::RegObj;
use EnsEMBL::Web::DBSQL::DBConnection;
eval{
require Bio::EnsEMBL::SimpleFeature;
require Bio::EnsEMBL::Analysis;
require Bio::EnsEMBL::DBSQL::DBAdaptor;
};
# Constants
Readonly my $current_assembly => 'NCBIM37';
Readonly my $new_assembly => 'NCBIM36';
Readonly my $host => '127.0.0.1';
Readonly my $port => '3309';
Readonly my $user => '????';
Readonly my $pass => '????';
Readonly my $dbname => 'mus_musculus_core_47_37';
# Extends BioMart::FormatterI
use base qw(BioMart::FormatterI);
# HTML templates
my $current_rowcount = 0; # keep track of number of rows printed out
Readonly my $FOOTER_TMPL => qq{</div>
};
Readonly my $HEADER_TMPL => q{<?xml version="1.0"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<title>%s</title>
<link rel="stylesheet" type="text/css" href="/martview/martview.css" />
</head>
<body>
<table>
};
Readonly my $ROW_START_TMPL1 => qq{<tr>\n};
Readonly my $ROW_START_TMPL2 => qq{<tr>\n};
Readonly my $HEADERFIELD_TMPL1 => qq{ <th>%s</th>\n};
Readonly my $HEADERFIELD_TMPL2 => qq{ <th>%s</th>\n};
Readonly my $NORMALFIELD_TMPL1 => qq{ <td>%s</td>\n};
Readonly my $ROW_END_TMPL => qq{</tr>\n};
sub _new {
my ($self) = @_;
$self->SUPER::_new();
# connect to database and get adaptors
my $db = EnsEMBL::Web::DBSQL::DBConnection->new( 'Mus_musculus', $ENSEMBL_WEB_REGISTRY->species_defs
)->get_DBAdaptor( 'core', 'Mus_musculus' );
$self->attr('db_adaptor',$db);
}
sub getFormatterDisplayName {
return 'Mouse 36 assembly (HTML)';
}
sub processQuery {
my ($self, $query) = @_;
$self->set('original_attributes',[@{$query->getAllAttributes()}])
if ($query->getAllAttributes());
$query = $self->setHTMLAttributes($query);
$query->addAttribute('strand');
$query->addAttribute('chromosome_name');
$self->set('query',$query);
return $query;
}
sub nextRow {
my $self = shift;
my $rtable = $self->get('result_table');
# print the data with urls if available
my $new_row;
my $row = $rtable->nextRow;
if (!$row){
return;
}
my $chromosome = $$row[-1];
my $strand = $$row[-2];
# convert coordinates to NCBI36 assembly
my @atts_to_convert = qw(
start_position
end_position
transcript_start
transcript_end
feat_chr_start
feat_chr_end
gene_chrom_start
gene_chrom_end
transcript_chrom_start
transcript_chrom_end
exon_chrom_start
exon_coding_end
exon_chrom_end
exon_coding_start
chromosome_location
);
my $attribute_order = $self->get('original_attributes');
my $attribute_number = 0;
my ($orig_attribute,$position,$new_position);
foreach (@$attribute_order){
$orig_attribute = $_->name;
foreach (@atts_to_convert){
if ($orig_attribute eq $_){
# covert coordinates
$position = $$row[$attribute_number];
next if (!$position);
my $db = $self->get('db_adaptor');
my $sa = $db->get_SliceAdaptor();
# create an analysis for the type of feature you wish to store
my $analysis = new Bio::EnsEMBL::Analysis(
-LOGIC_NAME => 'your_analysis'
);
my $slice_oldasm = $sa->fetch_by_region('chromosome', $chromosome, undef, undef,
undef, $current_assembly);
# create a new feature on the old assembly
my $feat = Bio::EnsEMBL::SimpleFeature->new(
-DISPLAY_LABEL => '',
-START => $position,
-END => $position,
-STRAND => $strand,
-SLICE => $slice_oldasm,
-ANALYSIS => $analysis,
);
# project feature to new assembly
my $feat_slice = $feat->feature_Slice;
my @segments;
if ($feat_slice){
@segments = @{ $feat->feature_Slice->project('chromosome', $new_assembly) };
}
# do some sanity checks on the projection results:
# discard the projected feature if
# 1. it doesn't project at all (no segments returned)
# 2. the projection is fragmented (more than one segment)
# 3. the projection doesn't have the same length as the original
# feature
if (scalar(@segments) != 1){
$new_position = '-';
}
elsif ($segments[0]->to_Slice()->length != $feat->length){
$new_position = '-';
}
elsif ($segments[0]->to_Slice()->seq_region_name ne $feat->slice->seq_region_name){
$new_position = '-';
}
else{
$new_position = $segments[0]->to_Slice()->start;
}
$$row[$attribute_number] = $new_position;
}
}
$attribute_number++;
}
my $new_row_length = @$row - 3;
$row = [@$row[0..$new_row_length]];
map { $_ = q{} unless defined ($_); } @$row;
my $attribute_positions = $self->get('attribute_positions');
my $attribute_url_positions = $self->get('attribute_url_positions');
my $attribute_url = $self->get('attribute_url');
#my $dataset1_end = $self->get('dataset1_end');
for (my $i = 0; $i < @{$attribute_positions}; $i++){
# superscripting for emma mart
$$row[$$attribute_positions[$i]] =~ s/\<(.*)\>/<span style="vertical-align:super;font-size:0.8em">$1<\/span>/;
if ($$attribute_url[$i]){
my @url_data = map {$$row[$_]} @{$$attribute_url_positions[$i]};
my $url_string = sprintf($$attribute_url[$i],@url_data);
push @{$new_row}, '<a href="'.$url_string.'" target="_blank">'.
$$row[$$attribute_positions[$i]]."</a>";
}
else{
push @{$new_row},$$row[$$attribute_positions[$i]];
}
}
$current_rowcount++;
my $fields_string = '';
map{ $fields_string .= sprintf ($NORMALFIELD_TMPL1, defined ($_) ? $_ : ''); } @{$new_row};
return ($current_rowcount % 2 == 0 ? $ROW_START_TMPL1 : $ROW_START_TMPL2)
. $fields_string
. $ROW_END_TMPL;
}
sub getDisplayNames {
my $self = shift;
my $original_attributes = $self->get('original_attributes');
my $dataset1_end = $self->get('dataset1_end');
my $query = $self->get('query');
my $registry = $query->getRegistry;
my $final_dataset_order = $query->finalDatasetOrder;
my @attribute_display_names;
my @original_dataset_attributes;
foreach my $dataset(reverse @$final_dataset_order){
foreach (@{$original_attributes}){
push @original_dataset_attributes,$_
if ($_->dataSetName eq $dataset);
}
}
foreach my $original_attribute(@original_dataset_attributes){
push @attribute_display_names, $original_attribute->displayName;
}
# print the display names
my $header_string = sprintf $HEADER_TMPL, '';
$header_string .= $ROW_START_TMPL1;
# map{ $header_string .=
# sprintf $HEADERFIELD_TMPL, $_ } @attribute_display_names;
map{ $header_string .= sprintf $HEADERFIELD_TMPL1, $_ } @attribute_display_names[0..$dataset1_end];
map{ $header_string .= sprintf $HEADERFIELD_TMPL2, $_ } @attribute_display_names[$dataset1_end+1..@attribute_display_names-1];
$header_string .= $ROW_END_TMPL;
return $header_string;
}
# Override empty-string returning method in superclass, to return proper
# table- and document-closing tags (to keep HTML valid).
sub getFooterText {
return q{
</table>
};
}
sub getMimeType {
return 'text/html';
}
1;
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