lib/CXGN/Primers.pm

   1 #!/usr/bin/perl
   2
   3 package CXGN::Primers;
   4
   5 use CXGN::DB::Connection;
   6 use strict;
   7
   8 sub get_sequence {
   9     my $sequence_name = shift;
  10
  11     my $dbh = CXGN::DB::Connection->new() or die "cannot connect: $!\n";
  12
  13     my $sequence =  &get_sequence_1($sequence_name,$dbh);
  14     if ($sequence eq "") {
  15         $sequence = &get_sequence_2($sequence_name,$dbh);
  16     }
  17
  18     $dbh->disconnect(42) or die "cannot disconnect: $!\n";
  19
  20     return $sequence;
  21 }
  22
  23 sub get_sequence_2 {
  24     my ($sequence_name,$dbh) = @_;
  25
  26     my $select = "select seq from unigene join unigene_member using "
  27         . "(unigene_id) join est using (est_id) where sequence_name = '$sequence_name';";
  28     my $sth = $dbh->prepare("$select");
  29     $sth->execute;
  30     my $sequence = $sth->fetchrow();
  31     $sth->finish;
  32
  33     return $sequence;
  34 }
  35
  36 sub get_sequence_1 {
  37     my ($sequence_name,$dbh) = @_;
  38
  39     my $select = "select seq from unigene_consensi join unigene "
  40         . "using (consensi_id) where sequence_name = '$sequence_name';";
  41     my $sth = $dbh->prepare("$select");
  42     $sth->execute;
  43     my $sequence = $sth->fetchrow();
  44     $sth->finish;
  45
  46     return $sequence;
  47 }
  48
  49 1;