mason/transcript/unigene/gene_family_info.mas

   1 <%doc>
   2
   3 =head1 NAME
   4
   5  gene_family.mas
   6  Mason component to show gene family data associated to an unigene
   7
   8 =cut
   9
  10 =head1 VERSION
  11
  12 0.1
  13
  14 =cut
  15
  16 =head1 SYNOPSIS
  17
  18 <& '/transcript/unigene/gene_family_info.mas', unigene => $unigene &>
  19
  20  where $unigene is CXGN::Transcript::Unigene object
  21
  22 =cut
  23
  24 =head1 DESCRIPTION
  25
  26  Another piece of mason code get the unigene data (gene family info) from the database and show it
  27  as table web_page;
  28  This code was taken from unigene.pl (originally added by Chenwei, 08/2005, slightly refactored, Lukas 9/2007)
  29
  30 =cut
  31
  32 =head 1 AUTHOR
  33
  34  Aureliano Bombarely (ab782@cornell.edu)
  35
  36 =cut
  37
  38 </%doc>
  39
  40
  41 <%args>
  42 $unigene
  43 </%args>
  44
  45
  46 <%perl>
  47
  48 use strict;
  49 use warnings;
  50
  51 use CXGN::Page::FormattingHelpers  qw/ info_section_html info_table_html columnar_table_html page_title_html html_break_string /;
  52
  53 my ($library_content, $library_html, @library_table);
  54
  55
  56 ## Get the object
  57 my $id =  $unigene->get_unigene_id();
  58
  59 ## If there aren't any unigene that comes from unigene_detail.mas, it will not do anything because the error message is given for the
  60 ## basic_detail.mas script
  61
  62 my $gene_family_html_content;
  63
  64 if (defined $id) {
  65
  66     my @families = $unigene->get_families();
  67
  68     my $gene_family_content;
  69     my @family_info;
  70     if (scalar(@families) > 0) {
  71         for my $family (@families) {
  72             my ($fam_id, $ivalue, $annotation, $count) = @{$family};
  73         if ($annotation) {
  74             $annotation =~ s/;/<br>/g;
  75             $annotation =~ s/,/<br>/g;
  76             $annotation =~ s/Molecular Function/ - Molecular Function/g;
  77             $annotation =~ s/Cellular Component/ - Cellular Component/g;
  78             $annotation =~ s/Biological Process/ - Biological Process/g;
  79         }
  80             my $family_link = '<a href="family.pl?family_id='.$fam_id.'">'.$fam_id."</a>";
  81             push @family_info, [$ivalue, $family_link, $annotation, $count];
  82         }
  83         $gene_family_content = columnar_table_html( headings => ['Family Build <br>(I value*)','Family ID', 'Annotation**','# Members'],
  84                                                     data     => \@family_info,
  85                                                     __align => ['c', 'c', 'l', 'c'],
  86                                                    );
  87
  88         $gene_family_content .= '<br> *i value: controls inflation, a process to dissipate family clusters. ';
  89         $gene_family_content .= 'At high i value, genes tend to be separated into different families.<br>';
  90         $gene_family_content .= '**Annotation: the most common InterPro annotation(s) of the Arabidopsis members in the family.<br>';
  91
  92     }
  93
  94     my $gf_count = scalar(@families);
  95     $gene_family_html_content = info_section_html( title        => "Gene Family (" . $gf_count . ")",
  96                                                    contents     => $gene_family_content,
  97                                                    collapsible  => 1,
  98                                                    collapsed    => 1, );
  99 }
 100
 101
 102 </%perl>
 103
 104 <% $gene_family_html_content %>