mason/feature/region_sequence.mas

   1 <%args>
   2     $feature
   3     $blast_url        => undef
   4     $max_display_size => 50_000
   5 </%args>
   6 <%perl>
   7
   8   my $seq;
   9
  10   #my @locs = $feature->featureloc_features(undef,{ prefetch => 'srcfeature' });
  11   my @locs = $feature->featureloc_features({locgroup => 0,},{ prefetch => 'srcfeature' });
  12   for my $loc ( @locs ) {
  13     if( my $src = $loc->srcfeature ) {
  14
  15         my $has_seq = $src->subseq(1,1);
  16
  17         if( $has_seq ) {
  18 </%perl>
  19             <div style="margin: 1em 3em">
  20 <%perl>
  21             # if the sequence is small enough to display
  22             if( $loc->fmax - $loc->fmin <= $max_display_size ) {
  23
  24                 my $seq = $src->trunc( $loc->fmin+1, $loc->fmax );
  25                 $seq->desc( location_string( $loc ) );
  26                 if( $loc->strand && $loc->strand == -1 ) {
  27                     $seq = $seq->revcom;
  28                     $seq->desc( $seq->desc.' (sequence from reverse strand)' );
  29                 }
  30
  31                 $seq->id( $feature->name );
  32
  33 </%perl>
  34
  35                 <& /sequence/with_markup.mas,
  36                    seq       => $seq,
  37                    width     => 80,
  38                    subdiv    => 10,
  39                    blast_url => $blast_url,
  40                  &>
  41
  42 %            } else { # otherwise, if the sequence is big
  43                 <p class="warning">Sequence region (<% location_string_html($loc) %>) too large to display.</p>
  44 %            }
  45 %            my ( $start, $end ) = $loc->strand == -1 ? ( $loc->fmax, $loc->fmin+1 ) : ( $loc->fmin+1, $loc->fmax );
  46              <% info_table_html(
  47                  __tableattrs => 'width="100%"',
  48                  __multicol   => 2,
  49                  'Download sequence region' => $m->scomp(
  50                      '/feature/sequence_download.mas',
  51                      feature      => $feature,
  52                      length       => $loc->fmax - $loc->fmin,
  53                      download_url => '/api/v1/sequence/download/single/'.$src->feature_id.".fasta?$start..$end",
  54                      ),
  55                  'Get flanking sequences on '.($src->name || 'feature_'.$src->feature_id) =>
  56                     $m->scomp('.flanking_download', loc => $loc ),
  57                 )
  58               %>
  59               </div>
  60 %      }
  61 %   }
  62 % }
  63
  64 <%once>
  65    use SGN::View::Feature qw/ location_string location_string_html /;
  66    use List::Util qw/ min max /;
  67    use List::MoreUtils qw/ pairwise /;
  68    use CXGN::Page::FormattingHelpers 'info_table_html';
  69
  70    sub upstream_downstream_options {
  71        my ( $loc ) = @_;
  72
  73        my $id         = $loc->srcfeature->feature_id;
  74        my $start      = $loc->fmin+1;
  75        my $end        = $loc->fmax;
  76        my $strand     = $loc->strand;
  77        my $src_length = $loc->srcfeature->length || 1e20;
  78
  79        my @increments = ( 1000, 3000, 5000 );
  80
  81        # calculate location strings for upstream and downstream regions
  82        my $upstream = [
  83            map location_string(
  84                $id,
  85                max( 1, $start - $_ ),
  86                max( 1, $start - 1  ),
  87                $strand
  88              ), @increments
  89          ];
  90
  91        my $downstream = [
  92            map location_string(
  93                $id,
  94                min( $end + 1,  $src_length ),
  95                min( $end + $_, $src_length ),
  96                $strand
  97              ), @increments
  98          ];
  99
 100        # upstream/downstream sense is reversed if feature is on the
 101        # reverse strand
 102        if( $strand == -1 ) {
 103            ( $upstream, $downstream ) = ( $downstream, $upstream );
 104        }
 105
 106        # decorate the upstream/downstream loc strings with text
 107        # descriptions for the dropdown
 108        my @upstream_desc   = map "$_ bp upstream",   @increments;
 109        my @downstream_desc = map "$_ bp downstream", @increments;
 110        $upstream   = [ pairwise { [$a, $b] } @$upstream,   @upstream_desc   ];
 111        $downstream = [ pairwise { [$a, $b] } @$downstream, @downstream_desc ];
 112
 113        return ( reverse(@$upstream), @$downstream );
 114    }
 115
 116 </%once>
 117
 118 <%def .flanking_download>
 119 <%args>
 120   $loc
 121 </%args>
 122     <form name="get_flanking_sequence" action="/api/v1/sequence/download/multi" method="GET">
 123       <input type="hidden" name="format" value="fasta" />
 124       <select name="s">
 125 %       for ( upstream_downstream_options( $loc ) ) {
 126 %          my ( $locstring, $description ) = @$_;
 127            <option value="<% $locstring %>"><% $description %></option>
 128 %       }
 129       </select>
 130       <input value="Download" type="submit" />
 131     </form>
 132
 133 </%def>