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