cgi-bin/secretom/search.pl

   1
   2 # quick hack to implement a secretom search...
   3 # most of this concerns Arabidopsis so we don't have anything in the SGN database...
   4
   5
   6
   7 use strict;
   8
   9 use CXGN::Page;
  10 use CXGN::Tools::Identifiers qw | link_identifier |;
  11 my $page = CXGN::Page->new();
  12 my ($query) = $page->get_encoded_arguments("query");
  13
  14 my $secretom_file_dir = '/data/prod/public/secretom/';
  15
  16 my $tabfile = 'Tair9RiceBrachyITAG1.tab';
  17
  18 $page->header();
  19
  20 print <<HTML;
  21
  22
  23 <center>
  24
  25
  26 <form>
  27
  28     <img src='/documents/img/secretom/secretom_logo.jpg' border="0" width="50%" /><br /><br />
  29
  30     Search<br /><br />
  31  <input type="text" name="query" value="$query" /><br /><br />
  32
  33     <input type="submit" value="Search" size="20" />
  34
  35 </center>
  36
  37 </form>
  38
  39 HTML
  40
  41     my @matches = ();
  42
  43
  44 if ($query) {
  45
  46     my @column_headers = (
  47         "locus name",
  48         "annotation",
  49         "protein length",
  50         "mol weight",
  51         "signalp-nn (Dscore)",
  52         "signalp-nn (YES if Dscore >= 0.43, NO otherwise)",
  53         "signalp-nn pred sp len",
  54         "signalp-hmm sp score",
  55         "signalp-hmm sa score",
  56         "signalp-hmm prediction (SP,SA or NS)",
  57         "targetP result (C,M,S,_)"
  58         );
  59
  60
  61     @matches = `grep -i \"$query\" $secretom_file_dir/$tabfile`; # this should be ok because we use get_encoded_arguments...
  62
  63     print "<br /><br />Your search \"<b>$query</b>\" return ".scalar(@matches)." matches. <br /><br />\n";
  64
  65     if (@matches) {
  66
  67
  68
  69
  70         print "Results: <br />\n";
  71         print qq | <table alt="Secretom Results"  > |;
  72
  73         print format_table_row(@column_headers);
  74         foreach my $match (@matches) {
  75             my @fields = (split /\t/, $match)[0,1,4,5,6,7,8,9,10,11,12];
  76             my $link = link_identifier($fields[0]);
  77             $fields[0] = $link if(defined $link);
  78             print format_table_row(@fields);
  79         }
  80         print "</table>\n";
  81
  82     }
  83 }
  84
  85
  86
  87 $page->footer();
  88
  89
  90 sub format_table_row {
  91     my @row = @_;
  92
  93     return "<tr><td class=\"boxbgcolor5\">".(join "</td><td  class=\"boxbgcolor5\">", @row)."</td></tr>\n";
  94
  95 }