mason/markers/genome.mas

   1 <%args>
   2 $marker
   3 </%args>
   4 <%init>
   5
   6 # look up gbrowse cross-refs for this marker, if any
   7 my @xrefs = map {
   8
   9     $_->xrefs({
  10         -types   => ['match'],
  11         -name    => 'SGN-M'.$marker->marker_id,
  12         -aliases => 1,
  13     })
  14
  15 } $c->enabled_feature('gbrowse2');
  16
  17 </%init>
  18
  19 <&| /page/info_section.mas, title => "Genomic locations" &>
  20 % if( @xrefs ) {
  21 % my @locations =
  22   <& /page/columnar_table.mas,
  23             headings=>["Genome Annotation", "Position(s)"],
  24             data=> [ map [ $_->data_source->description,
  25                            '<a href="'.$_->url.'">'
  26                            .join( ', ', (
  27                                map $_->seq_id.':'.$_->start.'..'.$_->end, @{$_->seqfeatures}
  28                                   )
  29                              )
  30                            .'</a>',
  31                           ],
  32                      @xrefs
  33                    ],
  34             __alt_freq   =>2,
  35             __alt_width  => 1,
  36             __alt_offset => 3,
  37             __align=> 'l'
  38   &>
  39 % }
  40 </&>
  41