lib/CXGN/Cview/Map_overviews/Individual.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map_overviews::Individual - a class to display genetic map overviews associated with individual that contain chromosome fragments from other accessions (such as ILs) or carry genes mapped between 2 flanking markers.
   6
   7 =head1 SYNOPSYS
   8
   9
  10 =head1 DESCRIPTION
  11
  12
  13 =head1 AUTHOR(S)
  14
  15 Lukas Mueller (lam87@cornell.edu)
  16
  17 =head1 VERSION
  18
  19
  20 =head1 LICENSE
  21
  22
  23 =head1 FUNCTIONS
  24
  25 This class implements the following functions:
  26
  27 =cut
  28
  29 use strict;
  30
  31 package CXGN::Cview::Map_overviews::Individual;
  32
  33 use CXGN::Cview::Map_overviews;
  34
  35 use base qw | CXGN::Cview::Map_overviews |;
  36
  37 =head2 function new
  38
  39   Synopsis:
  40   Arguments:
  41   Returns:
  42   Side effects:
  43   Description:
  44
  45 =cut
  46
  47 sub new {
  48     my $class = shift;
  49
  50     my $self = $class->SUPER::new(@_);
  51     my $individual_id = shift;
  52     $self->set_individual_id($individual_id);
  53     $self->render_map();
  54     if (!$self->get_cache()->is_valid() && !$self->get_chromosome_count()) {
  55         return undef;
  56     }
  57     return $self;
  58 }
  59
  60 =head2 accessors set_individual_id, get_individual_id
  61
  62   Property:
  63   Setter Args:
  64   Getter Args:
  65   Getter Ret:
  66   Side Effects:
  67   Description:
  68
  69 =cut
  70
  71 sub get_individual_id {
  72     my $self=shift;
  73     return $self->{individual_id};
  74 }
  75
  76 sub set_individual_id {
  77     my $self=shift;
  78     $self->{individual_id}=shift;
  79 }
  80
  81
  82 =head2 function render_map
  83
  84   Synopsis:
  85   Arguments:
  86   Returns:
  87   Side effects:
  88   Description:
  89   To Do: move this to the data adapter
  90
  91 =cut
  92
  93 sub render_map {
  94     my $self = shift;
  95     my $individual_id = $self->get_individual_id();
  96
  97     #$self->get_cache()->set_force(1); # during development
  98     $self->get_cache()->set_key("individual overview $individual_id");
  99     $self->get_cache()->set_expiration_time(); # should never expire...
 100     $self->get_cache()->set_map_name("overview");
 101
 102     if ($self->get_cache()->is_valid()) { return; }
 103
 104     my $IMAGE_WIDTH = 700;
 105
 106     # get chromosome number of the individual in question.
 107     my $chr_q = "SELECT count(distinct(linkage_group.lg_name)) FROM phenome.genotype
 108                  JOIN phenome.genotype_experiment using (genotype_experiment_id)
 109                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 110                  JOIN sgn.linkage_group using (map_version_id)
 111                  WHERE map_version.current_version='t' AND individual_id=?";
 112     my $chr_h = $self->prepare($chr_q);
 113     $chr_h->execute($individual_id);
 114     my ($chr_count) = $chr_h->fetchrow_array();
 115
 116     #print STDERR "Individual has $chr_count chromosomes.\n";
 117     $self->set_chromosome_count($chr_count);
 118     if (!$chr_count) { return; }
 119
 120     $self->set_horizontal_spacing( int($IMAGE_WIDTH/($chr_count+1)) );
 121
 122     my %lengths = ();
 123
 124     my $query = "SELECT lg_name, max(position), map_version.map_id FROM sgn.linkage_group
 125                    JOIN sgn.marker_location using (lg_id)
 126                    JOIN sgn.map_version on (map_version.map_version_id=linkage_group.map_version_id)
 127                    JOIN phenome.genotype_experiment on (map_version.map_id=genotype_experiment.reference_map_id)
 128                    JOIN phenome.genotype using (genotype_experiment_id)
 129                    WHERE genotype.individual_id=?
 130                          AND map_version.current_version='t'
 131                    GROUP BY lg_name, map_version.map_id";
 132
 133     #print STDERR "QUERY: $query\n";
 134
 135     my $sth = $self->prepare($query);
 136     $sth ->execute($self->get_individual_id());
 137     my $map_id = 0;
 138     while (my ($lg_name, $length, $reference_map_id) = $sth->fetchrow_array()) {
 139         #print STDERR "LENGTHS: $lg_name is $length long.\n";
 140         $lengths{$lg_name}=$length;
 141         $map_id=$reference_map_id;
 142     }
 143
 144
 145
 146     my @c = ();
 147 #    my %clen = $self->get_map()->get_linkage_group_lengths();
 148     $self->{map_image}=CXGN::Cview::MapImage->new("", 700, 200);
 149     foreach my $chr (0..($chr_count-1)) {
 150         #print STDERR "Generating chromosome $chr...\n";
 151         $c[$chr] = CXGN::Cview::Chromosome->new();
 152         $c[$chr]->set_vertical_offset(40);
 153         $c[$chr]->set_width(12);
 154         $c[$chr]->set_height(100);
 155         $c[$chr]->set_caption($chr+1);
 156         $c[$chr]->set_length($lengths{$chr+1});
 157         $c[$chr]->set_horizontal_offset(($chr+1) * $self->get_horizontal_spacing());
 158         $c[$chr]->set_hilite_color(100, 100, 200);
 159
 160         $self->{map_image}->add_chromosome($c[$chr]);
 161     }
 162
 163     # now get the fragments to be highlighted
 164     #
 165     my $query2 = "SELECT linkage_group.lg_name, position, type, zygocity_code FROM phenome.genotype
 166                  JOIN phenome.genotype_region USING(genotype_id)
 167                  JOIN phenome.genotype_experiment USING (genotype_experiment_id)
 168                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 169                  JOIN sgn.marker_location using(map_version_id)
 170                  JOIN sgn.marker_experiment using(location_id)
 171                  JOIN sgn.linkage_group ON (genotype_region.lg_id=linkage_group.lg_id)
 172                  WHERE map_version.current_version='t'
 173                    AND genotype_region.marker_id_ns=sgn.marker_experiment.marker_id
 174                  AND individual_id =? and genotype_experiment.preferred='t' ORDER BY position";
 175
 176  #   print STDERR "QUERY2: $query2\n";
 177
 178
 179     my $query3 = "SELECT linkage_group.lg_name, position  FROM phenome.genotype
 180                  JOIN phenome.genotype_region USING(genotype_id)
 181                  JOIN phenome.genotype_experiment USING (genotype_experiment_id)
 182                  JOIN sgn.map_version ON (genotype_experiment.reference_map_id=sgn.map_version.map_id)
 183                  JOIN sgn.marker_location using(map_version_id)
 184                  JOIN sgn.marker_experiment using(location_id)
 185                  JOIN sgn.linkage_group ON (genotype_region.lg_id=linkage_group.lg_id)
 186                  WHERE map_version.current_version='t'
 187                    -- AND phenome.genotype_region.lg_id=sgn.linkage_group.lg_id
 188                    AND marker_id_sn=sgn.marker_experiment.marker_id
 189                  AND individual_id =? and genotype_experiment.preferred='t' ORDER BY position";
 190
 191 #    print STDERR "QUERY3: $query3\n";
 192
 193     my $sth2 = $self-> prepare($query2);
 194     $sth2->execute($individual_id);
 195
 196     my $sth3 = $self-> prepare($query3);
 197     $sth3->execute($individual_id);
 198
 199     while (my ($chr1, $top_marker, $type, $zygocity_code) = $sth2->fetchrow_array()) {
 200         my ($chr2, $bottom_marker) = $sth3->fetchrow_array();
 201
 202         if ($type eq "map") {
 203             my $m = CXGN::Cview::Marker->new($c[$chr1-1]);
 204             $m->get_label()->set_hidden(1);
 205
 206             my @color = (200, 200, 200);
 207             if ($zygocity_code eq "a") { @color = (255, 0, 0); }
 208             if ($zygocity_code eq "b") { @color = (0, 0, 255); }
 209             if ($zygocity_code eq "c") { @color = (200, 100, 0); }
 210             if ($zygocity_code eq "d") { @color = (0, 100, 200); }
 211             if ($zygocity_code eq "h") { @color = (50, 50, 50); }
 212             $m->set_color(@color);
 213             $m->set_offset($top_marker);
 214             $c[$chr1-1]->add_marker($m);
 215             $c[$chr1-1]->set_url("/cview/view_chromosome.pl?chr_nr=$chr1&amp;map_id=$map_id&amp;show_ruler=1");
 216         }
 217
 218         elsif ("$chr1" eq "$chr2") {
 219
 220             my $m = CXGN::Cview::Marker::RangeMarker->new($c[$chr1-1]);
 221             #$m->get_label()->set_stacking_level(1);
 222 #           $m->set_label_side("right");
 223             $m->get_label()->set_name("IL");
 224
 225             my $offset = ($top_marker+$bottom_marker)/2;
 226             $m->set_offset($offset);
 227             $m->set_north_range($offset-$top_marker);
 228             $m->set_south_range($bottom_marker-$offset);
 229
 230             $c[$chr1-1]->add_marker($m);
 231             $m->set_hilite_chr_region(1);
 232             #$m->get_label()->set_url("/cview/view_chromosome.pl?map_id=5&cM_start=$top_marker&cM_end=$bottom_marker&show_zoomed=1");
 233             $c[$chr1-1]->set_url("/cview/view_chromosome.pl?chr_nr=$chr1&amp;map_id=$map_id&amp;cM_start=".($top_marker-1)."&amp;cM_end=".($bottom_marker+1)."&amp;show_zoomed=1&amp;show_ruler=1");
 234
 235             #print STDERR "Fragment: $offset, $top_marker, $bottom_marker\n";
 236         }
 237         else { warn "[Individual_overviews] $chr1 should be the same as $chr2...\n"; }
 238
 239     }
 240     $self->get_cache()->set_image_data( $self->{map_image}->render_png_string() );
 241     $self->get_cache()->set_image_map_data( $self->{map_image}->get_image_map("overview") );
 242
 243 }
 244
 245 =head2 function get_cache_key
 246
 247   Synopsis:
 248   Arguments:
 249   Returns:
 250   Side effects:
 251   Description:
 252
 253 =cut
 254
 255 sub get_cache_key {
 256     my $self = shift;
 257     return "Individual".$self->get_individual_id();
 258 }
 259
 260
 261 =head2 accessors set_chromosome_count, get_chromosome_count
 262
 263   Property:
 264   Setter Args:
 265   Getter Args:
 266   Getter Ret:
 267   Side Effects:
 268   Description:
 269
 270 =cut
 271
 272 sub get_chromosome_count {
 273     my $self=shift;
 274     return $self->{chromosome_count};
 275 }
 276
 277 sub set_chromosome_count {
 278     my $self=shift;
 279     $self->{chromosome_count}=shift;
 280 }
 281
 282
 283 package CXGN::Cview::Map_overviews::Individual_overview;
 284
 285 use base qw | CXGN::Cview::Map_overviews::Individual |;
 286
 287 sub new {
 288     my $class = shift;
 289     my $self = $class->SUPER::new(@_);
 290     return $self;
 291 }
 292
 293 return 1;