cgi-bin/phenome/qtl_traits.pl

   1
   2 =head1 DESCRIPTION
   3
   4 A tiny mini script to display a group of traits/cvterms
   5 that start with a given letter
   6
   7 =head1 AUTHOR
   8
   9 Isaak Y Tecle (iyt2@cornell.edu)
  10
  11 =cut
  12
  13 use strict;
  14
  15 use List::MoreUtils qw /uniq/;
  16
  17 use HTML::Entities;
  18
  19 use CXGN::Page;
  20 use CXGN::Page::FormattingHelpers qw(
  21   info_section_html
  22   page_title_html
  23   columnar_table_html
  24   info_table_html
  25 );
  26
  27 use CXGN::DB::Connection;
  28 use CXGN::Chado::Cvterm;
  29 use CXGN::Search::CannedForms;
  30
  31 my $page = CXGN::Page->new( "SGN QTL/Traits", "Isaak" );
  32 $page->header();
  33
  34 my $index = $page->get_arguments("index");
  35
  36 my $dbh       = CXGN::DB::Connection->new();
  37 my $qtl_tools = CXGN::Phenome::Qtl::Tools->new();
  38 my ( $all_traits, $all_trait_d ) = $qtl_tools->all_traits_with_qtl_data();
  39 my @all_traits = @{$all_traits};
  40 @all_traits = uniq(@all_traits);
  41 @all_traits =
  42   sort { $a <=> $b } @all_traits;
  43
  44 my @index_traits;
  45 foreach my $trait (@all_traits)
  46 {
  47     if ( $trait =~ /^$index/i )
  48     {
  49         push @index_traits, $trait;
  50
  51     }
  52 }
  53
  54 my @traits_list;
  55
  56 if (@index_traits)
  57 {
  58     foreach my $trait (@index_traits)
  59     {
  60         my $cvterm = CXGN::Chado::Cvterm::get_cvterm_by_name( $dbh, $trait );
  61         my $cvterm_id = $cvterm->get_cvterm_id();
  62         if ($cvterm_id)
  63         {
  64             push @traits_list,
  65               [
  66                 map { $_ } (
  67 qq |<a href=/chado/cvterm.pl?cvterm_id=$cvterm_id>$trait</a> |
  68                 )
  69               ];
  70         }
  71         else
  72         {
  73             my $t = CXGN::Phenome::UserTrait->new_with_name( $dbh, $trait );
  74             my $trait_id = $t->get_user_trait_id();
  75             push @traits_list,
  76               [
  77                 map { $_ } (
  78 qq |<a href=/phenome/trait.pl?trait_id=$trait_id>$trait</a> |
  79                 )
  80               ];
  81
  82         }
  83
  84     }
  85
  86 }
  87
  88 print page_title_html('List Traits with QTLs');
  89
  90 print info_section_html (
  91                           title    => encode_entities( qq|Traits beginning with "$index"| ),
  92                           contents => columnar_table_html (
  93                               data          => \@traits_list,
  94                               __align       => 'l',
  95                               __alt_freq    => 2,
  96                               __alt_width   => 1,
  97                               __cellpadding => 20,
  98                               ),
  99                         );
 100
 101 my $search = CXGN::Search::CannedForms::qtl_search_form();
 102
 103 print info_section_html (
 104                           title       => 'Search QTLs by trait names',
 105                           contents    => $search,
 106                           collapsible => 1,
 107                           collapsed   => 0,
 108                         );
 109 $page->footer();
 110
 111 #############
 112