mason/feature/types/gene.mas

   1 <%args>
   2     $feature
   3     $blast_url => undef
   4     $xrefs     => []
   5     $featurelocs
   6 </%args>
   7 <%once>
   8     use SGN::View::Feature 'mrna_cds_protein_sequence';
   9 </%once>
  10 <%perl>
  11     #my $reference   = $featurelocs ? $featurelocs->single->srcfeature : undef ;
  12     #getting only for primary featureloc
  13     my $reference   = $featurelocs ? $featurelocs->search({locgroup => 0,},)->single()->srcfeature() : undef ;
  14     my @mrnas       = grep $_->type->name eq 'mRNA', $feature->child_features;
  15     my $current_loc = $featurelocs ? $featurelocs->search({locgroup => 0,},)->single() : undef ;
  16 </%perl>
  17
  18 <& /feature/page_title.mas, feature => $feature &>
  19
  20 <&| /page/info_section.mas,
  21     title       => 'Gene',
  22     subtitle    => $feature->is_obsolete ? 'WARNING: This feature is obsolete, new data is available.' : '',
  23     collapsible => 1,
  24 &>
  25   <& /feature/feature_data.mas,
  26       feature          => $feature,
  27       description_from => \@mrnas,
  28       featurelocs      => $featurelocs,
  29   &>
  30
  31   <& /feature/properties.mas,
  32      feature => $feature,
  33    &>
  34
  35 </&>
  36
  37 <&| /page/info_section.mas,
  38    title       => 'Genome Viewer',
  39    collapsible => 1,
  40 &>
  41
  42         <& /feature/jbrowse_exact_match.mas, feature => $feature , src_feature => $reference &>
  43
  44 </&>
  45
  46
  47 <&| /page/info_section.mas,
  48    title       => 'Related features',
  49    collapsible => 1,
  50 &>
  51   <& /feature/related_features.mas,
  52       reference => $reference,
  53       feature   => $feature,
  54       omit_columns => ['organism'],
  55   &>
  56
  57 </&>
  58
  59
  60 <&| /page/info_section.mas,
  61         title       => 'Genomic sequence',
  62         subtitle    => 'unprocessed genomic sequence region underlying this gene',
  63         empty_message => 'Not available',
  64         collapsible => 1,
  65         collapsed   => 1,
  66 &>
  67
  68    <& /feature/region_sequence.mas,
  69        feature   => $feature,
  70        blast_url => $blast_url,
  71    &>
  72
  73 </&>
  74
  75 % for my $mrna ( @mrnas ) {
  76
  77   <&| /page/info_section.mas,
  78           title       => 'mRNA '. $mrna->name,
  79           collapsible => 1,
  80   &>
  81
  82     <&| /page/info_section.mas,
  83        title => 'Ontology terms',
  84        subtitle => 'terms associated with this mRNA',
  85        collapsible => 1,
  86        is_subsection => 1,
  87     &>
  88
  89       <& /feature/feature_cvterms.mas,
  90           feature   => $mrna,
  91       &>
  92
  93     </&>
  94
  95 %   my ( $mrna_sequence, $cds_sequence, $protein_sequence ) = @{(mrna_cds_protein_sequence( $mrna ))[0] || [] };
  96
  97     <&| /page/info_section.mas,
  98             title         => 'cDNA sequence',
  99             is_subsection => 1,
 100             subtitle      => 'spliced cDNA sequence, including UTRs',
 101             empty_message => 'Not available',
 102             collapsible   => 1,
 103             collapsed     => 1,
 104     &>
 105
 106 %  if( $mrna_sequence ) {
 107
 108      <div style="margin-left: 3em">
 109        <& /sequence/with_markup.mas,
 110           seq       => $mrna_sequence,
 111           width     => 80,
 112           subdiv    => 10,
 113           blast_url => $blast_url,
 114         &>
 115      </div>
 116      <div style="margin-top: 1em">
 117         <& /feature/sequence_download.mas,
 118              feature => $mrna,
 119          &>
 120      </div>
 121 % }
 122
 123     </&>
 124
 125     <&| /page/info_section.mas,
 126             title         => 'Protein sequence',
 127             is_subsection => 1,
 128             subtitle      => 'translated polypeptide sequence',
 129             empty_message => 'Not available',
 130             collapsible   => 1,
 131             collapsed     => 1,
 132     &>
 133
 134 %  if( $protein_sequence ) {
 135
 136      <div style="margin-left: 3em">
 137        <& /sequence/with_markup.mas,
 138           seq       => $protein_sequence,
 139           width     => 80,
 140           subdiv    => 10,
 141           blast_url => $blast_url,
 142         &>
 143      </div>
 144 %    if( $protein_sequence->can('feature_id') ) {
 145      <div style="margin-top: 1em">
 146         <& /feature/sequence_download.mas,
 147              feature => $protein_sequence,
 148          &>
 149      </div>
 150 %    }
 151 % }
 152
 153     </&>
 154
 155     <&| /page/info_section.mas,
 156         title         => 'Related features',
 157         is_subsection => 1,
 158         collapsible   => 1,
 159      &>
 160
 161        <& /feature/related_features.mas,
 162              feature   => $mrna,
 163              omit_columns => ['organism'],
 164        &>
 165
 166     </&>
 167
 168   </&>
 169 % }
 170
 171 <&| /page/info_section.mas,
 172      title       => 'Related views',
 173      collapsible => 1,
 174  &>
 175      <& /sitefeatures/mixed/xref_set/link.mas,
 176         xrefs   => $xrefs,
 177         exclude => 'gbrowse2',
 178       &>
 179 </&>