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 DESCRIPTION
  12
  13 The FPC data is currently stored in a berkeleydb database. It is accessed using the following methods:
  14
  15 my $db = Bio::DB::GFF->new( -adaptor => 'berkeleydb',
  16 -dsn => '/data/local/cxgn/core/sgn/documents/gbrowse/databases/fpc/SGN_2009');
  17
  18 and then you can do all the Bio::DB::GFF things with it, do 'perldoc Bio::DB::GFF' to see.
  19
  20 =head1 AUTHOR(S)
  21
  22 Lukas Mueller <lam87@cornell.edu>
  23
  24 =head1 FUNCTIONS
  25
  26 This class implements the following functions:
  27
  28 =cut
  29
  30 package CXGN::Cview::Map::SGN::Contig;
  31 use strict;
  32
  33 use Bio::DB::GFF;
  34 use File::Spec;
  35 use CXGN::Cview::Map::SGN::Genetic;
  36 use CXGN::Cview::Chromosome::Physical;
  37 use CXGN::Cview::Marker::Physical;
  38
  39
  40 use base qw | CXGN::Cview::Map::SGN::Genetic |;
  41
  42 =head2 function new
  43
  44   Synopsis:
  45   Arguments:    a database handle (preferably generated through
  46                 CXGN::DB::Connection) and a map id. Currently,
  47                 only one map_id is supported, with the alpha-
  48                 numeric id of "contig".
  49   Returns:
  50   Side effects:
  51   Description:
  52
  53 =cut
  54
  55 sub new {
  56     my $class = shift;
  57     my $dbh = shift;
  58     my $id = shift;
  59     my $args = shift;
  60
  61     my $db_version_id = get_db_id($dbh, $id);
  62     my $self = $class -> SUPER::new($dbh, $db_version_id);
  63
  64 #    if (!defined($self)) { return undef; }
  65     $self->set_preferred_chromosome_width(18);
  66     $self->set_short_name($args->{short_name});
  67     $self->set_long_name($args->{long_name});
  68     $self->{gbrowse_fpc} = $args->{gbrowse_fpc};
  69     $self->{temp_dir} = $args->{temp_dir} || '/tmp';
  70     $self->set_abstract($args->{abstract});
  71     $self->{marker_link} = $args->{marker_link};
  72     $self->set_id($id);
  73
  74
  75
  76     return $self;
  77 }
  78
  79
  80 =head2 function get_chromosome()
  81
  82   Synopsis:
  83   Arguments:
  84   Returns:
  85   Side effects:
  86   Description:
  87
  88 =cut
  89
  90 sub get_chromosome {
  91     my $self = shift;
  92     my $chr_nr = shift;
  93
  94     my $map_factory = CXGN::Cview::MapFactory->new($self->get_dbh());
  95     my $id = get_db_id($self->get_dbh(), $self->get_id());
  96     #print STDERR "get_chromosome $id.\n";
  97     my $genetic_map = $map_factory->create({map_version_id=>$id});
  98     my $genetic=$genetic_map->get_chromosome($chr_nr);
  99     my $chromosome = CXGN::Cview::Chromosome::Physical->new();
 100
 101     my $largest_offset = 0;
 102
 103
 104 #    my $gff = Bio::DB::GFF->new(
 105 #       -adaptor => 'berkeleydb',
 106 #       -dsn     => $self->{berkeley_db_path},
 107 #       );
 108     my (@gff) = $self->{gbrowse_fpc}->databases();
 109     if (@gff > 1) { die "Can't deal with multiple databases right now..."; }
 110     if (!@gff) {    die "No database found!"; }
 111     my ($gff) = @gff;
 112
 113     foreach my $m ($genetic->get_markers()) {
 114         $m->set_chromosome($chromosome);
 115         $chromosome->add_marker($m);
 116         my $offset = $m->get_offset();
 117         if ($offset > $largest_offset) {
 118             $largest_offset=$offset;
 119         }
 120         $m->hide();
 121
 122         my @gff_markers = $gff->features(-method => 'marker',
 123                        -attributes => { Name => $m->get_name() },
 124                        );
 125         my @contigs = ();
 126         foreach my $gm (@gff_markers) {
 127             @contigs = $gm->refseq();
 128         }
 129         my $count = 0;
 130         foreach my $c (@contigs) {
 131             my $contig = CXGN::Cview::Marker::Physical->new();
 132             $contig->set_chromosome($chromosome);
 133             $contig->set_name($c);
 134
 135             #my $url = "/gbrowse/gbrowse/sanger_tomato_fpc/?name=$c";
 136             my $url = $self->{gbrowse_fpc}->view_url({ name => $c });
 137             $contig->set_marker_name($c);
 138             $contig->set_marker_type("contig");
 139             $contig->set_url($url);
 140             $contig->set_offset($m->get_offset());
 141             $contig->get_label()->set_name($c);
 142             $contig->get_label()->set_url($url);
 143             $contig->set_tooltip("Contig: $c. Anchored to: ".($m->get_name()).".");
 144             $chromosome -> add_marker($contig);
 145             $count++;
 146         }
 147     }
 148     $chromosome->set_length($largest_offset);
 149     $self->{chr}->[$chr_nr]=$chromosome;
 150     return $chromosome;
 151
 152 }
 153
 154 =head2 function get_overview_chromosome()
 155
 156   Synopsis:
 157   Arguments:
 158   Returns:
 159   Side effects:
 160   Description:
 161
 162 =cut
 163
 164 sub get_overview_chromosome {
 165     my $self = shift;
 166     my $chr_nr = shift;
 167
 168     my $bargraph = CXGN::Cview::Chromosome::BarGraph->new();
 169
 170     my $largest_offset = 0;
 171
 172     my $chromosome = $self->get_chromosome($chr_nr);
 173
 174     foreach my $m ($chromosome->get_markers()) {
 175         if ($m->get_marker_type() eq "contig") {
 176             my $offset = $m->get_offset();
 177             $bargraph -> add_association("manual", $offset, 1);
 178             if ($offset>$largest_offset) { $largest_offset = $offset; }
 179         }
 180     }
 181     return $bargraph;
 182 }
 183
 184 =head2 function get_chromosome_connections()
 185
 186   Synopsis:
 187   Arguments:
 188   Returns:
 189   Side effects:
 190   Description:
 191
 192 =cut
 193
 194 sub get_chromosome_connections {
 195     my $self = shift;
 196     my $chr_nr = shift;
 197     my @list = ();
 198     # this map has no connections.!!!!
 199 #    push @list, { map_version_id=>CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id), lg_name=>$chr_nr, marker_count=>"?", short_name=>"F2-2000" };
 200     return @list;
 201 }
 202
 203 sub get_db_id {
 204     my $dbh = shift;
 205     my $id = shift;
 206     my $db_id = $id;
 207     $db_id=~s/^.*(\d+)$/$1/;
 208     return CXGN::Cview::Map::Tools::find_current_version($dbh, $db_id);
 209 }
 210
 211
 212 sub can_zoom {
 213     return 0;
 214 }
 215
 216 sub get_marker_link {
 217     my $self = shift;
 218     my $clone_id= shift;
 219     if ($clone_id) { return ""; }
 220     else { return ""; }
 221 }
 222
 223 sub get_marker_count {
 224     my $self = shift;
 225     my $chr_nr = shift;
 226
 227     my $tmp_file = "";
 228
 229     my @lengths = $self->cache_marker_counts();
 230     return $lengths[$chr_nr-1];
 231 }
 232
 233 sub cache_marker_counts {
 234     my $self = shift;
 235
 236     my @lengths = ();
 237     my $temp_file = File::Spec->catfile($self->{temp_dir}, 'contig'.$self->get_id()."_marker_counts.txt");
 238
 239     if (! -e ($temp_file)) {
 240         open(my $TEMP, ">$temp_file") || die "Can't open $temp_file for writing.";
 241         for my $c (1..12) {
 242             my $count = 0;
 243             my $chr = $self->get_chromosome($c);
 244             foreach my $m ($chr->get_markers()) {
 245                 if ($m->get_marker_name()=~ /^ctg/) {
 246                     $count++;
 247                 }
 248             }
 249             print $TEMP "$c\t$count\n";
 250
 251         }
 252     }
 253
 254     else {
 255         open(my $TEMP, "<$temp_file") || die "Can't open $temp_file for reading.";
 256         while (<$TEMP>) {
 257             chomp;
 258             my ($c, $length) = split /\t/;
 259             push @lengths, $length;
 260         }
 261
 262     }
 263     return @lengths;
 264 }
 265
 266 sub get_map_stats {
 267     my $self = shift;
 268
 269     my $count = 0;
 270     foreach my $c (1..12) {
 271         $count += $self->get_marker_count($c);
 272     }
 273
 274     return "$count contigs have been assigned to this map";
 275 }
 276
 277 =head2 get_abstract
 278
 279  Usage:
 280  Desc:
 281  Ret:
 282  Args:
 283  Side Effects:
 284  Example:
 285
 286 =cut
 287
 288 1;