bin/update_blast_names.pl

   1 #!/usr/bin/perl
   2
   3 use Getopt::Std;
   4 use Bio::Chado::Schema;
   5 use CXGN::DB::InsertDBH;
   6 use Data::Dumper;
   7 use File::Slurp qw | read_file |;
   8
   9 use vars qw | $opt_H $opt_D $opt_f |;
  10
  11 getopts('H:D:f:');
  12
  13 my $dbh = CXGN::DB::InsertDBH->new( {
  14     dbhost => $opt_H,
  15     dbname => $opt_D,
  16     } );
  17
  18 my $file = $opt_f;
  19 my @lines = read_file($file);
  20
  21 my $schema = Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() } );
  22
  23 eval {
  24     foreach my $l (@lines) {
  25
  26         chomp($l);
  27         $l =~ s/\r//g;
  28
  29         my ($old_name, $transcript_name, $species, $abbr) = split /\t/, $l;
  30
  31         my $q = "SELECT blast_db_id FROM sgn.blast_db WHERE title=?";
  32
  33         my $h = $dbh->prepare($q);
  34         $h->execute($old_name);
  35
  36         while (my ($blast_db_id) = $h->fetchrow_array()) {
  37             print STDERR "Found $old_name ($blast_db_id).\n";
  38             my $q2 = "UPDATE sgn.blast_db set title=? where blast_db_id=?";
  39             my $new_name = "$species ($abbr)";
  40             my $h2 = $dbh->prepare($q2);
  41             $h2->execute($new_name, $blast_db_id);
  42             print STDERR "Stored new name $new_name\n";
  43         }
  44     }
  45 };
  46
  47 if ($@) {
  48     print STDERR "An error occurred. Rolling everything back. ($@)\n";
  49     $dbh->rollback();
  50 }
  51
  52 else {
  53     print STDERR "Done. Committing...\n";
  54     $dbh->commit();
  55
  56 }