cgi-bin/scraps/fasta.pl

   1 #!/usr/bin/perl
   2 use CXGN::Scrap::AjaxPage;
   3 use CXGN::DB::Connection;
   4 use CXGN::UserList::Hotlist;
   5 #use CXGN::Login;
   6
   7 my $page = CXGN::Scrap::AjaxPage->new();
   8 my %args = $page->get_all_encoded_arguments();
   9
  10 $page->send_http_header;
  11 print $page->header();
  12
  13 print "<caller>Fasta</caller>\n";
  14
  15 #   Test high-latency conditions for AJAX:
  16 #       system("sleep 3");
  17
  18 my $type = $args{type} or $page->throw("Type must be specified");
  19 $type =~ /(protein)|(genomic)|(cdna)|(cds)/ or $page->throw("Invalid sequence type: $type");
  20
  21 my $agi_list = $args{agi_list} or $page->throw("Agi list must be sent");
  22
  23 my $fasta = "";
  24
  25 my $dbh = CXGN::DB::Connection->new("public");
  26
  27 my $sth = $dbh->prepare("SELECT $type FROM ara_sequence WHERE agi=?");
  28
  29 my @agis = split /::/, $agi_list;
  30
  31 foreach(@agis){
  32         $sth->execute($_);
  33         my $row = $sth->fetchrow_hashref;
  34         my $seq = $row->{$type};
  35         $seq =~ s/(\w{60})/$1\n/g;
  36         $fasta .= ">$_ | " . $type . "\n$seq\n";
  37 }
  38 print "<type>$type</type>\n";
  39 print "<fasta>$fasta\n</fasta>";
  40
  41 print $page->footer();