bin/load_trait_formula.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5 load_trait_formula.pl - loads formulas for computing derived traits
   6
   7 =head1 DESCRIPTION
   8
   9 load_trait_formula.pl -H [database host] -D [database name] load_trait_formula_file.txt
  10
  11 Options:
  12
  13  -H the database host
  14  -D the database name
  15
  16 load_trait_formula_file.txt: A file with two columns: trait name, trait formula.
  17
  18 If the trait name is found in the database, formula for computing the trait will be added as a cvtermprops.
  19
  20 =head1 AUTHOR
  21
  22 Alex Ogbonna <aco46@cornell.edu>
  23
  24 =cut
  25
  26
  27 use strict;
  28 use warnings;
  29 use Bio::Chado::Schema;
  30 use Getopt::Std;
  31 use CXGN::DB::InsertDBH;
  32 use SGN::Model::Cvterm;
  33
  34 our ($opt_H, $opt_D);
  35 getopts("H:D:");
  36 my $dbhost = $opt_H;
  37 my $dbname = $opt_D;
  38 my $file = shift;
  39 my @traits;
  40 my @formulas;
  41 my @array_ref;
  42
  43 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>"$dbhost",
  44                                    dbname=>"$dbname",
  45                                    dbargs => {AutoCommit => 1,
  46                                               RaiseError => 1,
  47                                    }
  48
  49                                  } );
  50
  51
  52 my $schema= Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() });
  53
  54 my $formula_cvterm = $schema->resultset("Cv::Cvterm")->create_with({
  55         name => "formula",
  56         cv   => "cvterm_property",
  57 });
  58
  59 my $type_id = $formula_cvterm->cvterm_id();
  60
  61 open (my $file_fh, "<", $file ) || die ("\nERROR: the file $file could not be found\n" );
  62
  63 my $header = <$file_fh>;
  64 while (my $line = <$file_fh>) {
  65     chomp $line;
  66
  67     my ($my_trait,$my_formula) = split("\t", $line);
  68         push @traits, $my_trait;
  69         push @formulas, $my_formula;
  70 }
  71
  72 for (my $n=0; $n<scalar(@traits); $n++) {
  73                 print STDERR $traits[$n]."\n";
  74     my $trait_cvterm = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($schema, $traits[$n]);
  75     if (!$trait_cvterm) {
  76         print STDERR "The trait $traits[$n] is not in the database. Skipping...\n";
  77         next();
  78     }
  79
  80     my $cvterm_id = $trait_cvterm->cvterm_id();
  81     my $new_prop= $trait_cvterm->create_cvtermprops({formula=>$formulas[$n]} , {} );
  82
  83 }