mason/locus/print_mrna_features.mas

   1 <%args>
   2     $feature
   3     $blast_url => undef
   4 </%args>
   5 <%once>
   6     use SGN::View::Feature 'mrna_cds_protein_sequence';
   7 </%once>
   8 <%perl>
   9     my @mrnas       = grep $_->type->name eq 'mRNA', $feature->child_features;
  10 </%perl>
  11
  12
  13 <&| /page/info_section.mas,
  14         title       => 'Genomic sequence',
  15         subtitle    => 'unprocessed genomic sequence region underlying this gene',
  16         empty_message => 'Not available',
  17         collapsible => 1,
  18         collapsed   => 1,
  19 &>
  20
  21    <& /feature/region_sequence.mas,
  22        feature   => $feature,
  23        blast_url => $blast_url,
  24    &>
  25
  26 </&>
  27
  28 % for my $mrna ( @mrnas ) {
  29
  30   <&| /page/info_section.mas,
  31           title       => 'mRNA '. $mrna->name,
  32           collapsible => 1,
  33   &>
  34
  35     <&| /page/info_section.mas,
  36        title => 'Ontology terms',
  37        subtitle => 'terms associated with this mRNA',
  38        collapsible => 1,
  39        is_subsection => 1,
  40     &>
  41
  42       <& /feature/feature_cvterms.mas,
  43           feature   => $mrna,
  44       &>
  45
  46     </&>
  47
  48 %   my ( $mrna_sequence, $cds_sequence, $protein_sequence ) = @{(mrna_cds_protein_sequence( $mrna ))[0] || [] };
  49
  50     <&| /page/info_section.mas,
  51             title         => 'cDNA sequence',
  52             is_subsection => 1,
  53             subtitle      => 'spliced cDNA sequence, including UTRs',
  54             empty_message => 'Not available',
  55             collapsible   => 1,
  56             collapsed     => 1,
  57     &>
  58
  59 %  if( $mrna_sequence ) {
  60
  61      <div style="margin-left: 3em">
  62        <& /sequence/with_markup.mas,
  63           seq       => $mrna_sequence,
  64           width     => 80,
  65           subdiv    => 10,
  66           blast_url => $blast_url,
  67         &>
  68      </div>
  69      <div style="margin-top: 1em">
  70         <& /feature/sequence_download.mas,
  71              feature => $mrna,
  72          &>
  73      </div>
  74 % }
  75
  76     </&>
  77
  78     <&| /page/info_section.mas,
  79             title         => 'Protein sequence',
  80             is_subsection => 1,
  81             subtitle      => 'translated polypeptide sequence',
  82             empty_message => 'Not available',
  83             collapsible   => 1,
  84             collapsed     => 1,
  85     &>
  86
  87 %  if( $protein_sequence ) {
  88
  89      <div style="margin-left: 3em">
  90        <& /sequence/with_markup.mas,
  91           seq       => $protein_sequence,
  92           width     => 80,
  93           subdiv    => 10,
  94           blast_url => $blast_url,
  95         &>
  96      </div>
  97 %    if( $protein_sequence->can('feature_id') ) {
  98      <div style="margin-top: 1em">
  99         <& /feature/sequence_download.mas,
 100              feature => $protein_sequence,
 101          &>
 102      </div>
 103 %    }
 104 %  }
 105     </&>
 106   </&>
 107 %}