Raw content of BioMart::Formatter::HTML_36 # $Id: HTML_36.pm,v 1.5 2007/10/15 15:52:26 ds5 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; 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 = new Bio::EnsEMBL::DBSQL::DBAdaptor( -HOST => $host, -PORT => $port, -USER => $user, -PASS => $pass, -DBNAME => $dbname); $self->attr('db_adaptor',$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;