mason/markers/rflp.mas

   1
   2 <%doc>
   3
   4 =head1 NAME
   5
   6 /markers/rflp.mas - a Mason component displaying information about rflp (known function genes) markers
   7
   8 =head1 ARGS
   9
  10 =head2 marker
  11
  12 a CXGN::Marker object.
  13
  14 =head1 AUTHOR
  15
  16 Robert Buels <rmb32@cornell.edu>
  17
  18 =cut
  19
  20 </%doc>
  21
  22 <%args>
  23 $marker
  24 </%args>
  25
  26 <%init>
  27 use CXGN::Page::FormattingHelpers qw/ info_table_html columnar_table_html /;
  28 use CXGN::Tools::Identifiers qw/ link_identifier /;
  29 use SGN::Controller::Marker;
  30
  31 sub fmt_sequence {
  32   my $seq = shift
  33     or return '<span class="ghosted">not available</span>';
  34   '<span class="sequence">'.CXGN::Page::FormattingHelpers::html_break_string($seq,90).'</span>'
  35 }
  36 sub fmt_rflp_image_link {
  37     my $marker = shift;
  38     my $l = SGN::Controller::Marker->rflp_image_link( $c, $marker )
  39         or return '<span class="ghosted">'.$marker->get_name.' image not available</span>';
  40     return '<a href="/marker/SGN-M'.$marker->marker_id.'/rflp_image/view">'.$marker->get_name.' RFLP image</a>';
  41 }
  42 sub len_pct {
  43     my ($len,$seq) = @_;
  44     return sprintf('%d (%0.1f%% of RFLP seq)',$len,$len/length($seq)*100);
  45 }
  46
  47 my $e_val_blast_cutoff = '1.0e-4';
  48 </%init>
  49
  50 % if( my $r = $marker->rflp_data() ) {
  51 %     my ($forward_unigene_matches, $reverse_unigene_matches) = $marker->rflp_unigene_matches( $r->{forward_seq_id}, $r->{reverse_seq_id} );
  52
  53       <&| /page/info_section.mas, title=>'RFLP details' &>
  54
  55          <% info_table_html( __border => 0, __multicol => 5,
  56               'Insert size'     => $r->{insert_size},
  57               'Vector'          => $r->{vector},
  58               'Cutting Site'    => $r->{cutting_site},
  59               'Drug Resistance' => $r->{drug_resistance},
  60               'Image'           => fmt_rflp_image_link( $marker ),
  61          )%>
  62          <% info_table_html( __border => 0,
  63               'Forward sequence' => fmt_sequence( $r->{forward_seq} ),
  64               'Reverse sequence' => fmt_sequence( $r->{reverse_seq} ),
  65          )%>
  66
  67       </&>
  68        <&| /page/info_section.mas, title => 'RFLP sequence matches to unigenes' &>
  69 %          if( @$forward_unigene_matches || @$reverse_unigene_matches ) {
  70                <% columnar_table_html(
  71                       headings => ['Unigene','e value','Match length (bp)','Strand'],
  72                       data     => [
  73                                     ( map [ link_identifier($_->[0]), $_->[1], len_pct($_->[2], $r->{forward_seq}), '+' ], @$forward_unigene_matches ),
  74                                     ( map [ link_identifier($_->[0]), $_->[1], len_pct($_->[2], $r->{reverse_seq}), '-' ], @$reverse_unigene_matches ),
  75                                   ],
  76                )%>
  77 %          }
  78        </&>
  79
  80 %}