[GENERAL] description = P. falciparum chromosome 11 db_adaptor = Bio::DB::GFF db_args = -adaptor memory -dir '/var/www/html/gbrowse/databases/MAL11' aggregators = transcript alignment orf plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest # Web site configuration info stylesheet = /gbrowse/gbrowse.css buttons = /gbrowse/images/buttons js = /gbrowse/js tmpimages = /gbrowse/tmp # where to link to when user clicks in detailed view link = AUTO # what image widths to offer image widths = 450 640 800 1024 # default width of detailed view (pixels) default width = 800 default features = Genes # The class of the feature that is used as the reference for all others # "Sequence" is the default - change it if you use something else reference class = Sequence # max and default segment sizes for detailed view max segment = 500000 default segment = 50000 # zoom levels zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 # whether to show the sources popup menu (0=false, 1=true; defaults to true) show sources = 1 # colors of the overview, detailed map and key overview bgcolor = lightgrey detailed bgcolor = lightgoldenrodyellow key bgcolor = beige # examples to show in the introduction examples = MAL11:370,500..410,000 # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ### # inside the section head = # at the top... header = # a footer footer = # Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = postgrid = sub { my ($gd, $panel) = @_; $gd->alphaBlending(0); $gd->saveAlpha(1); $panel->boxes(); # causes the layout to be calculated use Tie::IxHash; my %orthologs; my %location; my %drawn; my %newdrawn; for my $track (@{$panel->{tracks}}) { for my $part (@{$track->{parts}}) { my $feature = $part->{feature}; next unless $feature->isa("Bio::SeqFeatureI"); my @orthologs = $feature->get_tag_values("Ortholog"); next unless @orthologs; my $gene = $feature->name; for my $ortholog (@orthologs) { unless (exists $orthologs{$ortholog}) { tie(%{$orthologs{$ortholog}}, "Tie::IxHash"); } $orthologs{$ortholog}->{$gene}++; } my $yoffset = $panel->track_position($track); my $padleft = $panel->pad_left(); my ($x1, $y1, $x2, $y2) = $part->bounds(); $x1 += $padleft; $x2 += $padleft; $y1 += $yoffset - 2; $y2 += $yoffset + 2; $location{$gene} = [ $x1, $y1, $x2, $y2 ]; if (exists $orthologs{$gene}) { ORTHOLOGS : for my $ortholog (keys %{$orthologs{$gene}}) { unless (exists $location{$ortholog}) { warn "no location for $ortholog (ortholog of $gene)\n"; next ORTHOLOGS; } if ($drawn{$ortholog}) { for my $coortholog (@orthologs) { next ORTHOLOGS if $drawn{$ortholog}->{$coortholog}; } } $newdrawn{$ortholog}->{$gene}++; my ($ox1, $oy1, $ox2, $oy2) = @{$location{$ortholog}}; my $polygon = GD::Polygon->new(); $polygon->addPt($ox1, $oy2); $polygon->addPt($ox2, $oy2); $polygon->addPt($x2, $y1); $polygon->addPt($x1, $y1); $gd->filledPolygon($polygon, $gd->colorAllocateAlpha($panel->color_name_to_rgb("darkgray"), 100)); # $gd->openPolygon($polygon, $gd->colorAllocateAlpha($panel->color_name_to_rgb("lightsteelblue"), 0)); $gd->line($ox1, $oy2, $x1, $y1, $panel->translate_color("lightsteelblue")); $gd->line($ox2, $oy2, $x2, $y1, $panel->translate_color("lightsteelblue")); } } } while (my ($key, $value) = each %newdrawn) { $drawn{$key} = { %{$drawn{$key} || {}}, %{$value || {}} }; } %newdrawn = undef; } } # Default glyph settings [TRACK DEFAULTS] glyph = generic height = 8 bgcolor = cyan fgcolor = cyan label density = 25 bump density = 100 ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks [Genes] feature = gene:annotation glyph = processed_transcript bgcolor = blue font2color = darkgrey height = 10 description = 1 label = 1 link = http://plasmodb.org/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=$name key = Annotated Genes citation = Structural and functional gene annotation provided by the sequencing centers. [SyntenyGenes] feature = gene:syntenyVivaxMC glyph = processed_transcript bgcolor = lightblue fgcolor = blue font2color = darkgrey height = 10 description = 1 label = 1 link = http://plasmodb.org/showRecord.do?name=GeneRecordClasses.GeneRecordClass&primary_key=$name key = Synteny Genes citation = Structural and functional gene annotation provided by the sequencing centers.