cgi-bin/content/library_info.pl

   1 use CXGN::Page;
   2
   3 use strict;
   4 use CXGN::DB::Connection;
   5
   6 library_info_main();
   7
   8 sub library_info_main {
   9
  10      our $page = CXGN::Page->new( "SGN Library Info", "Lukas");
  11
  12      my ($library) = $page -> get_arguments("library");
  13      my $db = CXGN::DB::Connection->new();
  14
  15      my $query = "SELECT organism.organism_name, types.comment as type, library_name, library_shortname, development_stage, treatment_conditions, tissue, cultivar, accession,cloning_host, comments, authors, contact_information, cloning_kit, rs1, rs2, library.library_id
  16                   FROM library, organism, types
  17                   WHERE library.organism_id=organism.organism_id and library.type=types.type_id and library_shortname=?";
  18      my $sth = $db -> prepare($query);
  19      $sth -> execute($library);
  20
  21      my $libraries ="";
  22      my $lib =$sth-> fetchrow_hashref();
  23
  24
  25
  26      if (!exists($$lib{library_shortname})) {
  27
  28          $page -> header();
  29
  30          my $temp_value = "<h4>Library Detail Page</h4> Library \n";
  31
  32     if ($library) {
  33         $temp_value = $temp_value."\"<b>$library</b>\" \n";
  34 }
  35
  36 $temp_value = $temp_value."unknown. Sorry! Please try again.<br /><br /><br /><br /><br />\n";
  37
  38          print $temp_value;
  39
  40          $page -> footer();
  41          return;
  42      }
  43
  44      my $query2 = "SELECT count(*) from clone, seqread, est WHERE clone.clone_id=seqread.clone_id and seqread.read_id=est.read_id and clone.library_id=? and est.status=0 and est.flags=0";
  45
  46      my $sth2 = $db->prepare($query2);
  47      $sth2->execute($lib->{library_id});
  48      my ($seq_count) = $sth2->fetchrow_array();
  49
  50      my $query3 = "SELECT count(*) from clone WHERE clone.library_id=?";
  51      my $sth3 = $db -> prepare($query3);
  52      $sth3 -> execute($lib->{library_id});
  53      my ($clone_count) = $sth3 -> fetchrow_array();
  54
  55      my $query4 = "SELECT avg(hqi_length), stddev(hqi_length) FROM clone, seqread, est, qc_report where clone.library_id=? and clone.clone_id=seqread.clone_id and seqread.read_id=est.read_id and est.est_id=qc_report.est_id and est.flags=0 and est.status=0 group by clone.library_id";
  56      my $sth4 = $db -> prepare($query4);
  57      $sth4 -> execute($lib->{library_id});
  58      my ($average_seqlen, $std_dev) = $sth4 -> fetchrow_array();
  59      $average_seqlen = sprintf "%4.1f", $average_seqlen;
  60      $std_dev = sprintf "%4.1f", $std_dev;
  61
  62      $page -> header();
  63
  64      print <<HTML;
  65
  66      <h4>Library Detail Page for $library</h4>
  67      <table>
  68      <tr><td width="180">Short Name:</td><td>$$lib{library_shortname}</td></tr>
  69      <tr><td>Organism:</td><td>$$lib{organism_name}</td></tr>
  70      <tr><td>Library Name: </td><td>$$lib{library_name}</td></tr>
  71      <tr><td>Total Sequences: </td><td>$seq_count sequences from $clone_count clones</td></tr>
  72      <tr><td>Average Sequence Length:</td><td>$average_seqlen (Standard deviation $std_dev)</td></tr>
  73      <tr><td>Type:</td><td>$$lib{type}</td></tr>
  74      <tr><td>Tissue:</td><td>$$lib{tissue}</td></tr>
  75      <tr><td>Development Stage:</td><td>$$lib{development_stage}</td></tr>
  76      <tr><td valign="top">Treatment Conditions:</td><td>$$lib{treatment_conditions}</td></tr>
  77      <tr><td>Cloning Host:</td><td>$$lib{cloning_host}</td></tr>
  78      <tr><td>Cloning Kit: </td><td>$$lib{cloning_kit}</td></tr>
  79      <tr><td valign="top">Comments</td><td>$$lib{comments}</td></tr>
  80      <tr><td valign="top">Authors</td><td>$$lib{authors}</td></tr>
  81      <tr><td valign="top">Contact Information</td><td>$$lib{contact_information}</td></tr>
  82      </table>
  83      <br /><br /><br /><br /><br />
  84
  85 HTML
  86
  87      $page -> footer();
  88  }