lib/CXGN/Phenotypes/TrialPhenotype.pm

   1
   2 package CXGN::Phenotypes::TrialPhenotype;
   3
   4
   5 =head1 NAME
   6
   7 CXGN::Phenotypes::TrialPhenotype - an object to handle retrieving of trial phenotype and field information.
   8
   9 =head1 USAGE
  10
  11 my $phenotypes_heatmap = CXGN::Phenotypes::TrialPhenotype->new(
  12         bcs_schema=>$schema,
  13         trial_id=>$trial_id,
  14         trait_id=>$trait_id
  15 );
  16 my @phenotype = $phenotypes_heatmap->get_trial_phenotypes_heatmap();
  17
  18 =head1 DESCRIPTION
  19
  20
  21 =head1 AUTHORS
  22
  23
  24 =cut
  25
  26
  27
  28 use strict;
  29 use warnings;
  30 use Moose;
  31 use Data::Dumper;
  32 use SGN::Model::Cvterm;
  33 use List::MoreUtils qw | :all !before !after |;
  34 use CXGN::Trial;
  35
  36 BEGIN { extends 'Catalyst::Controller'; }
  37
  38 has 'bcs_schema' => (
  39         isa => 'Bio::Chado::Schema',
  40         is => 'rw',
  41         required => 1,
  42 );
  43
  44 has 'trial_id' => (
  45         isa => 'Int',
  46         is => 'rw',
  47     required => 1,
  48 );
  49
  50 has 'trait_id' => (
  51         isa => 'Int',
  52         is => 'rw',
  53     required => 1,
  54 );
  55
  56 sub get_trial_phenotypes_heatmap {
  57     my $self = shift;
  58     my $schema = $self->bcs_schema;
  59     my $trial_id = $self->trial_id;
  60     my $trait_id = $self->trait_id;
  61         my $rep_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'replicate', 'stock_property')->cvterm_id();
  62     my $block_number_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'block', 'stock_property')->cvterm_id();
  63     my $plot_number_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot number', 'stock_property')->cvterm_id();
  64     my $row_number_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'row_number', 'stock_property')->cvterm_id();
  65         my $col_number_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'col_number', 'stock_property')->cvterm_id();
  66     my $plot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
  67     my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
  68
  69         my %columns = (
  70           stock_id => 'plot.stock_id',
  71           trial_id=> 'project.project_id',
  72           trait_id=> 'cvterm.cvterm_id',
  73       row_number=> 'row_number.value::int',
  74       col_number=> 'col_number.value::int',
  75       rep=> 'rep.value',
  76           plot_number=> 'plot_number.value::INT',
  77           block_number=> 'block_number.value',
  78       phenotype_value=> 'phenotype.value',
  79           phenotype_id=> 'phenotype.phenotype_id',
  80       plot_name=> 'plot.uniquename AS plot_name',
  81       accession_name=> 'accession.uniquename',
  82       from_clause=> " FROM stock as plot JOIN stock_relationship ON (plot.stock_id=subject_id)
  83       JOIN cvterm as plot_type ON (plot_type.cvterm_id = plot.type_id)
  84       JOIN stock as accession ON (object_id=accession.stock_id AND accession.type_id = $accession_type_id)
  85       LEFT JOIN stockprop AS rep ON (plot.stock_id=rep.stock_id AND rep.type_id = $rep_type_id)
  86       LEFT JOIN stockprop AS block_number ON (plot.stock_id=block_number.stock_id AND block_number.type_id = $block_number_type_id)
  87           LEFT JOIN stockprop AS col_number ON (plot.stock_id=col_number.stock_id AND col_number.type_id = $col_number_type_id)
  88           LEFT JOIN stockprop AS row_number ON (plot.stock_id=row_number.stock_id AND row_number.type_id = $row_number_type_id)
  89       LEFT JOIN stockprop AS plot_number ON (plot.stock_id=plot_number.stock_id AND plot_number.type_id = $plot_number_type_id)
  90       JOIN nd_experiment_stock ON(nd_experiment_stock.stock_id=plot.stock_id)
  91       JOIN nd_experiment ON (nd_experiment_stock.nd_experiment_id=nd_experiment.nd_experiment_id)
  92       LEFT JOIN nd_experiment_phenotype ON (nd_experiment_phenotype.nd_experiment_id=nd_experiment.nd_experiment_id)
  93       LEFT JOIN phenotype USING(phenotype_id)
  94       LEFT JOIN cvterm ON (phenotype.cvalue_id=cvterm.cvterm_id)
  95       LEFT JOIN dbxref ON (cvterm.dbxref_id = dbxref.dbxref_id)
  96       LEFT JOIN db USING(db_id)
  97       JOIN nd_experiment_project ON (nd_experiment_project.nd_experiment_id=nd_experiment.nd_experiment_id)
  98       JOIN project USING(project_id)",
  99     );
 100
 101         my $select_clause = "SELECT  DISTINCT ".$columns{'stock_id'}.", ".$columns{'plot_name'}.", ".$columns{'accession_name'}.", ".$columns{'plot_number'}.", ".$columns{'block_number'}.", ".$columns{'rep'}.", ".$columns{'row_number'}.", ".$columns{'col_number'}.", ".$columns{'phenotype_value'}.", ".$columns{'phenotype_id'}."";
 102
 103         my $from_clause = $columns{'from_clause'};
 104
 105         my $order_clause = " ORDER BY 7, 8, 4 ASC";
 106         my $numeric_regex = '^-?[0-9]+([,.][0-9]+)?$';
 107         my $numeric_regex_2 = '/^\s*$/';
 108
 109         my @where_clause;
 110
 111         if ($trial_id && $trait_id){
 112                 push @where_clause, " (". $columns{'trait_id'}." in ($trait_id) OR ". $columns{'trait_id'}." is NULL )";
 113                 #push @where_clause, $columns{'trait_id'}." in ($trait_id)";
 114                 push @where_clause, "plot.type_id in ($plot_type_id)";
 115                 push @where_clause, $columns{'trial_id'}." in ($trial_id)";
 116                 #push @where_clause, " (". $columns{'phenotype_value'}." ~\'$numeric_regex\' OR ". $columns{'phenotype_value'}." is NULL )";
 117                 push @where_clause, $columns{'phenotype_value'}." ~\'$numeric_regex\' ";
 118         }
 119
 120     my $where_clause = " WHERE " . (join (" AND " , @where_clause));
 121         my  $q = $select_clause . $from_clause . $where_clause . $order_clause;
 122
 123         my $h = $schema->storage->dbh()->prepare($q);
 124     $h->execute();
 125     my $result = [];
 126         my (@col_No, @row_No, @pheno_val, @plot_Name, @stock_Name, @plot_No, @block_No, @rep_No, @msg, %results, @phenoID);
 127
 128         while (my ($id, $plot_name, $stock_name, $plot_number, $block_number, $rep, $row_number, $col_number, $value, $pheno_id) = $h->fetchrow_array()) {
 129                 if (!$row_number && !$col_number){
 130                         if ($block_number){
 131                                 $row_number = $block_number;
 132                         }elsif ($rep && !$block_number ){
 133                                 $row_number = $rep;
 134                         }
 135                 }
 136                 my $plot_popUp = $plot_name."\nplot_No:".$plot_number."\nblock_No:".$block_number."\nrep_No:".$rep."\nstock:".$stock_name."\nvalue:".$value;
 137         push @$result,  {plotname => $plot_name, stock => $stock_name, plotn => $plot_number, blkn=>$block_number, rep=>$rep, row=>$row_number, col=>$col_number, pheno=>$value, plot_msg=>$plot_popUp, pheno_id=>$pheno_id} ;
 138                 push @col_No, $col_number;
 139                 push @row_No, $row_number;
 140                 push @pheno_val, $value;
 141                 push @plot_Name, $plot_name;
 142                 push @stock_Name, $stock_name;
 143                 push @plot_No, $plot_number;
 144                 push @block_No, $block_number;
 145                 push @rep_No, $rep;
 146         push @phenoID, $pheno_id;
 147                 push @msg, "plot_No:".$plot_number."\nblock_No:".$block_number."\nrep_No:".$rep."\nstock:".$stock_name."\nvalue:".$value;
 148     }
 149
 150         # my ($min_col, $max_col) = minmax @col_No;
 151         # my ($min_row, $max_row) = minmax @row_No;
 152         # my (@unique_col,@unique_row);
 153         # for my $x (1..$max_col){
 154         #       push @unique_col, $x;
 155         # }
 156         # for my $y (1..$max_row){
 157         #       push @unique_row, $y;
 158         # }
 159
 160     my $false_coord;
 161         if ($col_No[0] == ""){
 162         @col_No = ();
 163         $false_coord = 'false_coord';
 164                 my @row_instances = uniq @row_No;
 165                 my %unique_row_counts;
 166                 $unique_row_counts{$_}++ for @row_No;
 167         my @col_number2;
 168         for my $key (keys %unique_row_counts){
 169             push @col_number2, (1..$unique_row_counts{$key});
 170         }
 171         for (my $i=0; $i < scalar(@$result); $i++){
 172             @$result[$i]->{'col'} = $col_number2[$i];
 173             push @col_No, $col_number2[$i];
 174         }
 175         }
 176
 177     my ($min_col, $max_col) = minmax @col_No;
 178         my ($min_row, $max_row) = minmax @row_No;
 179         my (@unique_col,@unique_row);
 180         for my $x (1..$max_col){
 181                 push @unique_col, $x;
 182         }
 183         for my $y (1..$max_row){
 184                 push @unique_row, $y;
 185         }
 186
 187     my $trial = CXGN::Trial->new({
 188                 bcs_schema => $schema,
 189                 trial_id => $trial_id
 190         });
 191         my $data = $trial->get_controls();
 192
 193         #print STDERR Dumper($data);
 194
 195         my @control_name;
 196         foreach my $cntrl (@{$data}) {
 197                 push @control_name, $cntrl->{'accession_name'};
 198         }
 199         #print STDERR Dumper(\@$result);
 200         #print STDERR Dumper(\@plot_No);
 201
 202         %results = (
 203         col => \@col_No,
 204         row => \@row_No,
 205         pheno => \@pheno_val,
 206         plotName => \@plot_Name,
 207         stock => \@stock_Name,
 208         plot => \@plot_No,
 209         block => \@block_No,
 210         rep => \@rep_No,
 211         result => $result,
 212         plot_msg => \@msg,
 213         col_max => $max_col,
 214         row_max => $max_row,
 215         unique_col => \@unique_col,
 216         unique_row => \@unique_row,
 217     false_coord => $false_coord,
 218     phenoID => \@phenoID,
 219     controls => \@control_name
 220         );
 221     print STDERR "Search End:".localtime."\n";
 222         #print STDERR Dumper($result);
 223     return \%results;
 224 }
 225
 226 1;