[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 <head></head> 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.