lib/CXGN/Phenotypes/Exact.pm

   1 package CXGN::Phenotypes::Exact;
   2
   3 =head1 NAME
   4
   5 CXGN::Phenotypes::Exact - an object to retrieve the exact phenotypes and plot/plant names for a given trial id
   6
   7 =head1 SYNOPSIS
   8
   9 my $exact_obj = CXGN::Phenotypes::Exact->new({
  10     bcs_schema => $schema,
  11     trial_id => 1
  12 });
  13 my $exact_phenotypes = $exact_obj->search();
  14
  15 $exact_phenotypes is a hashref of hashrefs, where each phenotyped_trait is a key whose value is another hash where each plot_name is a key and trait value is the value
  16
  17 =head1 AUTHORS
  18
  19 bje24
  20
  21 =cut
  22
  23 use strict;
  24 use warnings;
  25 use Moose;
  26 use Try::Tiny;
  27 use Data::Dumper;
  28 use SGN::Model::Cvterm;
  29
  30 has 'bcs_schema' => ( isa => 'Bio::Chado::Schema',
  31     is => 'rw',
  32     required => 1,
  33 );
  34
  35 has 'trial_id' => (
  36         isa => 'Int',
  37         is => 'rw',
  38     required => 1,
  39 );
  40
  41 has 'data_level' => (
  42     is => 'ro',
  43     isa => 'Str',
  44     default => 'plot',
  45 );
  46
  47 sub search {
  48     my $self = shift;
  49     my $schema = $self->bcs_schema;
  50     my $trial_id = $self->trial_id;
  51     my $data_level = $self->data_level;
  52
  53     my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $data_level, 'stock_type')->cvterm_id();
  54
  55     my $h = $schema->storage->dbh->prepare("SELECT stock.name, (((cvterm.name::text || '|'::text) || db.name::text) || ':'::text) || dbxref.accession::text AS trait, phenotype.value
  56         FROM project
  57         JOIN nd_experiment_project USING(project_id)
  58         JOIN nd_experiment_stock AS all_stocks ON(nd_experiment_project.nd_experiment_id = all_stocks.nd_experiment_id)
  59         JOIN stock USING(stock_id)
  60         JOIN nd_experiment_stock AS my_stocks ON(stock.stock_id = my_stocks.stock_id)
  61         JOIN nd_experiment_phenotype ON(my_stocks.nd_experiment_id = nd_experiment_phenotype.nd_experiment_id)
  62         JOIN phenotype USING(phenotype_id)
  63         JOIN cvterm ON(phenotype.cvalue_id = cvterm.cvterm_id)
  64         JOIN dbxref ON cvterm.dbxref_id = dbxref.dbxref_id JOIN db ON dbxref.db_id = db.db_id
  65         WHERE project_id = ? AND stock.type_id = ?
  66         GROUP BY 1,2,3;");
  67
  68     $h->execute($trial_id, $stock_type_id);
  69
  70     my %exact_phenotypes;
  71     while (my ($stock, $synonym, $value) = $h->fetchrow_array()) {
  72         $exact_phenotypes{$synonym}{$stock} = $value;
  73     }
  74
  75     return \%exact_phenotypes;
  76 }
  77
  78 1;