lib/CXGN/Cview/Map/SGN/Contig.pm

   1 =head1 NAME
   2
   3 CXGN::Cview::Map::SGN::Contig - a class to generate maps of contigs aligned to the genome
   4
   5 =head1 SYNOPSYS
   6
   7  my $map = CXGN::Cview::Map::SGN::Contig->new($dbh, $id);
   8  my $chr = $map->get_chromosome(1);
   9  # etc...
  10
  11 =head1 AUTHOR(S)
  12
  13 Lukas Mueller <lam87@cornell.edu>
  14
  15 =head1 FUNCTIONS
  16
  17 This class implements the following functions:
  18
  19 =cut
  20
  21 package CXGN::Cview::Map::SGN::Contig;
  22 use strict;
  23 use warnings;
  24
  25 use File::Spec;
  26 use CXGN::Cview::MapFactory;
  27 use CXGN::Cview::Map::SGN::Genetic;
  28 use CXGN::Cview::Chromosome::Physical;
  29 use CXGN::Cview::Marker::Physical;
  30
  31 use CatalystX::GlobalContext '$c';
  32
  33 use base qw | CXGN::Cview::Map::SGN::Genetic |;
  34
  35 =head2 function new
  36
  37   Synopsis:
  38   Arguments:    a database handle (preferably generated through
  39                 CXGN::DB::Connection) and a map id. Currently,
  40                 only one map_id is supported, with the alpha-
  41                 numeric id of "contig".
  42   Returns:
  43   Side effects:
  44   Description:
  45
  46 =cut
  47
  48 sub new {
  49     my $class = shift;
  50     my $dbh = shift;
  51     my $id = shift;
  52     my $args = shift;
  53
  54     my $db_version_id = get_db_id($dbh, $id);
  55     my $self = $class -> SUPER::new($dbh, $db_version_id);
  56
  57     $self->set_preferred_chromosome_width(18);
  58     $self->set_short_name($args->{short_name});
  59     $self->set_long_name($args->{long_name});
  60     $self->{gbrowse_fpc} = $args->{gbrowse_fpc};
  61     $self->{temp_dir} = $args->{temp_dir} || '/tmp';
  62     $self->set_abstract($args->{abstract});
  63     $self->{marker_link} = $args->{marker_link};
  64     $self->set_id($id);
  65
  66     return $self;
  67 }
  68
  69
  70 =head2 function get_chromosome()
  71
  72   Synopsis:
  73   Arguments:
  74   Returns:
  75   Side effects:
  76   Description:
  77
  78 =cut
  79
  80 sub get_chromosome {
  81     my $self = shift;
  82     my $chr_nr = shift;
  83
  84     my $map_factory = CXGN::Cview::MapFactory->new($self->get_dbh());
  85     my $id = get_db_id($self->get_dbh(), $self->get_id());
  86     my $genetic_map = $map_factory->create({map_version_id=>$id});
  87     my $genetic=$genetic_map->get_chromosome($chr_nr);
  88     my $chromosome = CXGN::Cview::Chromosome::Physical->new();
  89
  90     my $largest_offset = 0;
  91
  92     my @gff = $self->{gbrowse_fpc}->databases()
  93       or $c->throw(
  94           public_message    => "Map not found.",
  95           developer_message => 'No gbrowse_fpc databases found',
  96           notify            => 1,
  97           is_server_error   => 0,
  98           is_client_error   => 0,
  99          );
 100
 101     if ( @gff > 1 ) { die "Can't deal with multiple databases right now..." }
 102
 103     my ($gff) = @gff;
 104
 105     for my $m ($genetic->get_markers()) {
 106         $m->set_chromosome($chromosome);
 107         $chromosome->add_marker($m);
 108         my $offset = $m->get_offset();
 109         if ($offset > $largest_offset) {
 110             $largest_offset=$offset;
 111         }
 112         $m->hide();
 113
 114         my @gff_markers = $gff->features(-method => 'marker',
 115                        -attributes => { Name => $m->get_name() },
 116                        );
 117         my @contigs = ();
 118         for my $gm (@gff_markers) {
 119             @contigs = $gm->refseq();
 120         }
 121         my $count = 0;
 122         for my $c (@contigs) {
 123             my $contig = CXGN::Cview::Marker::Physical->new();
 124             $contig->set_chromosome($chromosome);
 125             $contig->set_name($c);
 126
 127             #my $url = "/gbrowse/gbrowse/sanger_tomato_fpc/?name=$c";
 128             my $url = $self->{gbrowse_fpc}->view_url({ name => $c });
 129             $contig->set_marker_name($c);
 130             $contig->set_marker_type("contig");
 131             $contig->set_url($url);
 132             $contig->set_offset($m->get_offset());
 133             $contig->get_label()->set_name($c);
 134             $contig->get_label()->set_url($url);
 135             $contig->set_tooltip("Contig: $c. Anchored to: ".($m->get_name()).".");
 136             $chromosome -> add_marker($contig);
 137             $count++;
 138         }
 139     }
 140     $chromosome->set_length($largest_offset);
 141     $self->{chr}->[$chr_nr]=$chromosome;
 142     return $chromosome;
 143
 144 }
 145
 146 =head2 function get_overview_chromosome()
 147
 148   Synopsis:
 149   Arguments:
 150   Returns:
 151   Side effects:
 152   Description:
 153
 154 =cut
 155
 156 sub get_overview_chromosome {
 157     my $self = shift;
 158     my $chr_nr = shift;
 159
 160     my $bargraph = CXGN::Cview::Chromosome::BarGraph->new();
 161
 162     my $largest_offset = 0;
 163
 164     my $chromosome = $self->get_chromosome($chr_nr);
 165
 166     for my $m ($chromosome->get_markers()) {
 167         if ($m->get_marker_type() eq "contig") {
 168             my $offset = $m->get_offset();
 169             $bargraph -> add_association("manual", $offset, 1);
 170             if ($offset>$largest_offset) { $largest_offset = $offset; }
 171         }
 172     }
 173     return $bargraph;
 174 }
 175
 176 =head2 function get_chromosome_connections()
 177
 178   Synopsis:
 179   Arguments:
 180   Returns:
 181   Side effects:
 182   Description:
 183
 184 =cut
 185
 186 sub get_chromosome_connections {
 187     my $self = shift;
 188     my $chr_nr = shift;
 189     my @list = ();
 190     # this map has no connections.!!!!
 191 #    push @list, { map_version_id=>CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id), lg_name=>$chr_nr, marker_count=>"?", short_name=>"F2-2000" };
 192     return @list;
 193 }
 194
 195 sub get_db_id {
 196     my $dbh = shift;
 197     my $id = shift;
 198     my $db_id = $id;
 199     $db_id=~s/^.*(\d+)$/$1/;
 200     return CXGN::Cview::Map::Tools::find_current_version($dbh, $db_id);
 201 }
 202
 203
 204 sub can_zoom {
 205     return 0;
 206 }
 207
 208 sub get_marker_link {
 209     my $self = shift;
 210     my $clone_id= shift;
 211     if ($clone_id) { return ""; }
 212     else { return ""; }
 213 }
 214
 215 sub get_marker_count {
 216     my $self = shift;
 217     my $chr_nr = shift;
 218
 219     my $tmp_file = "";
 220
 221     my @lengths = $self->cache_marker_counts();
 222     return $lengths[$chr_nr-1];
 223 }
 224
 225 sub cache_marker_counts {
 226     my $self = shift;
 227
 228     my @lengths = ();
 229     my $temp_file = File::Spec->catfile($self->{temp_dir}, 'contig'.$self->get_id()."_marker_counts.txt");
 230
 231     if (! -e ($temp_file)) {
 232         open(my $TEMP, '>', $temp_file) or die "Can't open $temp_file for writing: $!";
 233         for my $c (1..12) {
 234             my $count = 0;
 235             my $chr = $self->get_chromosome($c);
 236             for my $m ($chr->get_markers()) {
 237                 if ($m->get_marker_name()=~ /^ctg/) {
 238                     $count++;
 239                 }
 240             }
 241             print $TEMP "$c\t$count\n";
 242
 243         }
 244     }
 245
 246     else {
 247         open(my $TEMP, '<', $temp_file) or die "Can't open $temp_file for reading: $!";
 248         while (<$TEMP>) {
 249             chomp;
 250             my ($c, $length) = split /\t/;
 251             push @lengths, $length;
 252         }
 253
 254     }
 255     return @lengths;
 256 }
 257
 258 sub get_map_stats {
 259     my $self = shift;
 260
 261     my $count = 0;
 262     for my $c (1..12) {
 263         $count += $self->get_marker_count($c);
 264     }
 265
 266     return "$count contigs have been assigned to this map";
 267 }
 268
 269 =head2 get_abstract
 270
 271  Usage:
 272  Desc:
 273  Ret:
 274  Args:
 275  Side Effects:
 276  Example:
 277
 278 =cut
 279
 280 1;