bin/load_trait_formula.pl

   1 #!/usr/bin/perl
   2
   3 use strict;
   4 use warnings;
   5 use Bio::Chado::Schema;
   6 use Getopt::Std;
   7 use CXGN::DB::InsertDBH;
   8 use SGN::Model::Cvterm;
   9
  10 our ($opt_H, $opt_D);
  11 getopts("H:D:");
  12 my $dbhost = $opt_H;
  13 my $dbname = $opt_D;
  14 my $file = shift;
  15 my @traits;
  16 my @formulas;
  17 my @array_ref;
  18
  19 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>"$dbhost",
  20                                    dbname=>"$dbname",
  21                                    dbargs => {AutoCommit => 1,
  22                                               RaiseError => 1,
  23                                    }
  24
  25                                  } );
  26
  27
  28 my $schema= Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() });
  29
  30 my $formula_cvterm = $schema->resultset("Cv::Cvterm")->create_with({
  31         name => "formula",
  32         cv   => "cvterm_property",
  33 });
  34
  35 my $type_id = $formula_cvterm->cvterm_id();
  36
  37 open (my $file_fh, "<", $file ) || die ("\nERROR: the file $file could not be found\n" );
  38
  39 my $header = <$file_fh>;
  40 while (my $line = <$file_fh>) {
  41     chomp $line;
  42
  43     my ($my_trait,$my_formula) = split("\t", $line);
  44         push @traits, $my_trait;
  45         push @formulas, $my_formula;
  46 }
  47
  48 for (my $n=0; $n<scalar(@traits); $n++) {
  49                 print STDERR $traits[$n]."\n";
  50     my $trait_cvterm = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $traits[$n]);
  51     if (!$trait_cvterm) {
  52         print STDERR "The trait $traits[$n] is not in the database. Skipping...\n";
  53         next();
  54     }
  55
  56     my $cvterm_id = $trait_cvterm->cvterm_id();
  57     my $new_prop= $trait_cvterm->create_cvtermprops({formula=>$formulas[$n]} , {} );
  58
  59 }