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#!/usr/bin/perl -w
# $Id: gbrowse_img,v 1.7 2009-08-31 19:46:38 lstein Exp $
use strict;
use Bio::Graphics::Browser2;
use Bio::Graphics::Browser2::Render::HTML;
use Bio::Graphics::Browser2::Util;
use Bio::Graphics::Karyotype;
use Digest::MD5 'md5_hex';
# call with following arguments:
# source database source
# type list of feature mnemonics
# options track options, in format mnemonic+option+mnemonic+option...
# name landmark or range to display, in format Name:start..stop
# width desired width of image, in pixels (height cannot be set)
# add a feature to superimpose on top of the image
# in format: reference+type+name+start..stop,start..stop,start..stop
# multiple "add" arguments are allowed
# style stylesheet for added features
# h_region region(s) to hilight
# h_feat feature(s) to hilight
umask 022;
my $fcgi = Bio::Graphics::Browser2::Render->fcgi_request;
my $modperl = $ENV{MOD_PERL};
my $init;
if ($modperl && !$init++) {
$SIG{USR1} = $SIG{PIPE} = $SIG{TERM} = sub {
my $sig = shift;
my $time = localtime;
print STDERR "[$time] [notice] GBrowse FastCGI process caught sig$sig. Exiting... (pid $$)\n";
CORE::exit 0
if ($fcgi) {
my $FCGI_DONE = 0;
$SIG{USR1} = $SIG{PIPE} = $SIG{TERM} = sub {
my $sig = shift;
my $time = localtime;
print STDERR "[$time] [notice] gbrowse_img FastCGI process caught sig$sig. Exiting... (pid $$)\n";
my %sys_env = %ENV;
while (!$FCGI_DONE) {
my $status = $fcgi->Accept;
next unless $status >= 0;
%ENV = ( %sys_env, %ENV );
my $globals = Bio::Graphics::Browser2->open_globals;
my $gbi = GBrowse_img->new($globals);
else {
my $globals = Bio::Graphics::Browser2->open_globals;
exit 0;
package GBrowse_img;
use CGI qw(param start_html end_html
p h1 path_info escape img);
use File::Spec;
use File::Temp 'tmpnam','tempfile','tempdir';
use Bio::Graphics::Browser2::Shellwords;
use constant DEBUG => 0;
use constant MAX_SEGMENT => 1_000_000;
use constant TOO_MANY_SEGMENTS => 500;
use constant PANEL_GAP => 3;
sub new {
my $class = shift;
my $globals = shift;
my $render = Bio::Graphics::Browser2::Render::HTML->new($globals);
return bless {render => $render},ref $class || $class;
sub run {
my $self = shift;
my $render = $self->render;
unless (param()) {
print $self->header();
print $self->usage();
$render->set_source() && exit; # may cause a redirect and exit
if ($render->data_source->must_authenticate
&& !$self->session->private) {
my $base = $render->globals->gbrowse_url;
print $self->header();
print CGI->h1('Authentication required. Please log into',CGI->a({-href=>$base},'GBrowse'),'from this computer.');
# notice that there is no explicit flush() of the session/state, and therefore the
# changes to the session are not stored.
warn join ' ',$render->potential_tracks if DEBUG;
# self-documentation feature: dump out tab-delimited list of mnemonics and keys
if (param('list')) {
$self->dump_sources($render) if param('list') eq 'sources';
$self->dump_types($render) if param('list') eq 'types';
if (param('debug')) {
sub render { shift->{render} }
sub session { shift->render->session }
sub cookie { shift->render->create_cookie }
sub source { shift->render->data_source }
sub destroy { my $self = shift;
undef $self->{render};
sub header {
my $self = shift;
if (@_ == 1) {
unshift @_,'-type';
my $cookie = $self->cookie();
return CGI::header(-cookie => $cookie,
sub dump_sources {
my $self = shift;
my $source = $self->source;
print $self->header('text/plain');
print "## Sources\n";
print join "\n",$source->globals->data_sources,"\n";
sub dump_types {
my $self = shift;
my $render = $self->render;
my $source = $self->source;
print $self->header('text/plain');
print "## Feature types for source ",$source->name,"\n";
my @labels = grep {!/:/ and !/^_/} $source->labels;
my %default = map {$_=>1} $source->default_labels;
for my $l (@labels) {
my $d = $default{$l} ? 'default' : '';
my $key = $render->setting($l=>'key')||'';
print join("\t",$l,$key,$d),"\n";
sub dump_state {
my $self = shift;
my $render = $self->render;
print $self->header('text/plain');
print "## Current state for debugging\n";
print "Source: ",$self->source->name,"\n";
print "Segment: ",$render->segment,"\n";
print "Labels: ",join(' ',$render->detail_tracks),"\n";
sub render_image {
my $self = shift;
my $render = $self->render;
my $renderer = $render->get_panel_renderer;
my $format = param('format') || 'GD';
my $flip = param('flip') || 0;
my $embed = param('embed');
if (my @regions = param('h_region')) {
$render->state->{h_region} = \@regions;
my $convert_to_pdf;
if ($format eq 'PDF' && `which inkscape`) {
$format = 'GD::SVG';
$format = 'GD::SVG' if $format eq 'SVG';
$format = 'GD' if $embed;
my ($img_data,$map) = $render->region->feature_count > 1
? $self->render_multiple($renderer,$format,$flip,$embed)
: $self->render_tracks ($renderer,$format,$flip,$embed);
my $seg = $render->segment;
my $fname = $seg ? $seg->seq_id.':'.$seg->start.'..'.$seg->end : "NA";
if ($embed) {
my $url = $renderer->source->generate_image($img_data);
my $js = $render->data_source->globals->js_url;
my @scripts = map { {src=>"$js/$_"} }
qw(balloon.js balloon.config.js yahoo-dom-event.js);
print $self->header(-type=>'text/html');
print start_html(-script=>\@scripts),
-src => $url,
-usemap => "#gbrowse2_img_map"}
elsif ($format eq 'GD') {
print $self->header(-type=>'image/png',
-content_disposition => "filename=$fname.png");
print $img_data->png;
elsif ($format eq 'GD::SVG' && $convert_to_pdf) {
print $self->header(-type=>'application/pdf',
-content_disposition => "filename=$fname.pdf");
my ($infh,$in) = tempfile(UNLINK=>0,SUFFIX=>'.svg');
my ($outfh,$out) = tempfile(UNLINK=>0,SUFFIX=>'.pdf');
print $infh $img_data or die "$in: $!";
close $infh;
system "inkscape -z --without-gui --export-pdf=$out $in 3<&1 1>&2 2>&3 | grep -v GDK_IS_DISPLAY";
open (my $fh,'<',$out) or die "$out: $!";
while (<$fh>) {print $_}
close $fh;
unlink $in,$out;
elsif ($format eq 'GD::SVG') {
print $self->header(-type => 'application/svg+xml',
-content_disposition => "filename=$fname.svg");
print $img_data;
else {
print $self->header('text/plain');
print "unknown format $format\n";
sub render_multiple {
my $self = shift;
my ($renderer,$format,$flip,$embed) = @_;
my $features = $self->render->region->features;
my $karyotype = Bio::Graphics::Karyotype->new(source => $self->render->data_source,
language => $self->render->language);
my $panels = $karyotype->generate_panels($format);
my (@gds,@seqids);
for my $seqid (keys %$panels) {
push @gds,$panels->{$seqid}{panel}->gd;
push @seqids,$seqid;
my $img_data = $self->consolidate_images(\@gds,undef,undef,'horizontal',\@seqids);
return ($img_data,undef);
sub render_tracks {
my $self = shift;
my ($renderer,$format,$flip,$embed) = @_;
my $render = $self->render;
my $external = $render->external_data;
warn 'visible = ',join ' ',$render->visible_tracks if DEBUG;
my @labels = $render->expand_track_names($render->detail_tracks);
warn "labels = ",join ',',@labels if DEBUG;
my @track_types = map {shellwords($_)} (param('t'),param('type'),param('track'));
my $h_callback = make_hilite_callback(param('h_feat'));
# If no tracks specified, we want to see all tracks with this feature
if (!@track_types) { @track_types = @labels; }
unshift @track_types,'_scale';
my $result = $renderer->render_track_images(
labels => \@track_types,
external_features => $external,
section => 'detail',
cache_extra => [$format,param('h_feat'),param('h_region')],
image_class => $format,
flip => $flip,
hilite_callback => $h_callback || undef,
-key_style => 'between',
-suppress_key => 0,
warn "returned labels = ",join ',',%$result if DEBUG;
# Previously - @labels (caused drawing more tracks than asked for)
my @image_data = @{$result}{grep {$result->{$_}} @track_types};
my @gds = map {$_->{gd} } @image_data;
my @map_data = map {$_->{map}} @image_data;
my $img_data = $self->consolidate_images(\@gds);
my $map = $self->consolidate_maps (\@map_data, \@gds) if $embed;
return ($img_data,$map);
sub calculate_composite_bounds {
my $self = shift;
my ($gds,$orientation) = @_;
warn "consolidating ",scalar @$gds," GD objects" if DEBUG;
my $height = 0;
my $width = 0;
if ($orientation eq 'vertical') {
for my $g (@$gds) {
warn "g=$g" if DEBUG;
next unless $g;
$height += ($g->getBounds)[1]; # because GD::SVG is missing the width() and height() methods
$width ||= ($g->getBounds)[0];
} elsif ($orientation eq 'horizontal') {
for my $g (@$gds) {
warn "g=$g" if DEBUG;
next unless $g;
$height = ($g->getBounds)[1] if $height < ($g->getBounds)[1];
$width += ($g->getBounds)[0];
return ($width,$height);
sub consolidate_images {
my $self = shift;
my ($gds,$width,$height,$orientation,$labels) = @_;
$orientation ||= 'vertical';
($width,$height) = $self->calculate_composite_bounds($gds,$orientation)
unless defined $width && defined $height;
warn "consolidating ",scalar @$gds," GD objects" if DEBUG;
return $gds->[0]->isa('GD::SVG::Image')
? $self->_consolidate_svg($width,$height,$gds,$orientation,$labels)
: $self->_consolidate_gd ($width,$height,$gds,$orientation,$labels);
sub make_hilite_callback {
my @feature_names = @_;
return unless @feature_names;
my %colors;
foreach (@feature_names) {
my ($name,$color) = split '@';
$color ||= 'yellow';
$colors{$name} = $color;
return sub {
my $feature = shift;
my $color;
# if we get here, we select the search term for highlighting
my %names = map {lc $_=> 1}
return unless %names;
$color ||= $colors{$_} foreach keys %names;
return $color;
sub _consolidate_gd {
my $self = shift;
my ($width,$height,$gds,$orientation,$labels) = @_;
my $class = ref($gds->[0]);
(my $fontclass = $class)=~s/::Image//;
my $lineheight = $fontclass->gdMediumBoldFont->height;
my $charwidth = $fontclass->gdMediumBoldFont->width;
$height += $lineheight if $orientation eq 'horizontal';
my $gd = $class->new($width,$height,1);
my $white = $gd->colorAllocate(255,255,255);
my $black = $gd->colorAllocate(0,0,0);
eval {
my $bg = $gds->[0]->getPixel(0,0);
my @bg = $gds->[0]->rgb($bg);
my $i = $gd->colorAllocate(@bg);
my $offset = 0;
if ($orientation eq 'vertical') {
for my $g (@$gds) {
next unless $g;
$offset += ($g->getBounds)[1];
} else {
for my $g (@$gds) {
next unless $g;
if ($labels) {
my $l = shift @$labels;
$offset+(($g->getBounds)[0]-$charwidth*length $l)/2,
$offset += ($g->getBounds)[0];
return $gd;
# because the GD::SVG copy() method is broken
sub _consolidate_svg {
my $self = shift;
my ($width,$height,$gds,$orientation,$labels) = @_;
my $image_height = $height;
if ($labels) {
my $font = GD::SVG->gdMediumBoldFont;
my $charwidth = $font->width;
my $lineheight=$font->height;
$image_height += $lineheight;
for my $gd (@$gds) {
my $l = shift @$labels;
my $black = $gd->colorAllocate(0,0,0);
(($gd->getBounds)[0]-$charwidth*length $l)/2,
my $svg = qq(<?xml version="1.0" encoding="UTF-8" standalone="yes"?>\n\n);
$svg .= qq(<svg height="$image_height" width="$width" xmlns="" xmlns:xlink="">\n);
if ($orientation eq 'vertical') {
my $offset = 0;
for my $g (@$gds) {
my $s = $g->svg;
my $current_height = 0;
foreach (split "\n",$s) {
if (m!</svg>!) {
elsif (/<svg.+height="([\d.]+)"/) {
$current_height = int($1+0.5);
$svg .= qq(<g transform="translate(0,$offset)">\n);
elsif ($current_height) {
$svg .= "$_\n";
$svg .= "</g>\n" if $current_height;
$offset += $current_height;
$svg .= qq(</svg>\n);
} else {
my $offset = 0;
for my $g (@$gds) {
my $s = $g->svg;
my $current_width = 0;
foreach (split "\n",$s) {
if (m!</svg>!) {
elsif (/<svg.+width="([\d.]+)"/) {
$current_width = int($1+0.5);
my $height = $height - ($g->getBounds)[1];
$svg .= qq(<g transform="translate($offset,$height)">\n);
elsif ($current_width) {
$svg .= "$_\n";
$svg .= "</g>\n" if $current_width;
$offset += $current_width;
$svg .= qq(</svg>\n);
# munge fonts slightly for systems that don't have Helvetica installed
$svg =~ s/font="Helvetica"/font="san-serif"/gi;
$svg =~ s/font-size="11"/font-size="9"/gi;
$svg =~ s/font-size="13"/font-size="12"/gi;
return $svg;
sub consolidate_maps {
my $self = shift;
my ($maps,$gds) = @_;
my $offset = 0;
my @integrated_list = 'gbrowse2_img';
for (my $i=0;$i<@$maps;$i++) {
my $data = $maps->[$i];
shift @$data;
for (@$data) {
my ($name,$x1,$y1,$x2,$y2,@rest) = split "\t";
$y1 += $offset;
$y2 += $offset;
push @integrated_list,join "\t",($name,$x1,$y1,$x2,$y2,@rest);
$offset += ($gds->[$i]->getBounds)[1];
return Bio::Graphics::Browser2::RenderPanels->map_html(\@integrated_list);
sub usage {
return <<'END';
<h1>gbrowse_img - CGI script to generate genome images via the Generic Genome Browser</h1>
&lt;img src=";width=400"&gt;
<i>Will generate this picture:</i>
<img src=";width=400">
&lt;a href=""&gt;list&lt;/a&gt;
<i>Will return this document:</i>
## Sources
&lt;a href=""&gt;types&lt;/a&gt;
<i>Will return this document:</i>
## Feature types for source c_elegans
LOCI:overview Landmarks default
RNAZ RNAz non-coding RNA genes
CG Gene Models default
CDS Coding Segments
RNA Predicted non-coding RNAs
HISTORICAL Obsolete gene models
GENEFINDER GeneFinder Predictions
TWINSCAN Twinscan Predictions
GENEMARKHMM GeneMarkHMM Predictions
This CGI script is an interface to the Generic Genome Browser for the
purpose of retrieving dynamic images of a region of the genome. It
can be used as the destination of an &lt;img&gt; tag like this:
&lt;img src=""&gt;
The script can also be used to superimpose one or more external
features onto the display, for example for the purpose of displaying
BLAST hits, an STS or a knockout in the context of the genome.
<h2>CGI arguments</h2>
The script recognizes the following CGI arguments, which can be passed
either as GET or POST argument=value pairs. Argument pairs must be
separated by semicolons (preferred) or by ampersands. Many of the
options have one-letter aliases that can be used to reduce URL
<table border="1">
<tr> <td>name</td> <td>q</td> <td>genomic landmark or range</td></tr>
<tr> <td>type</td> <td>t</td> <td>tracks to include in image</td></tr>
<tr> <td>width</td> <td>w</td> <td>desired width of image</td></tr>
<tr> <td>options</td> <td>o</td> <td>list of track options (compact, labeled, etc)</td></tr>
<tr> <td>abs</td> <td>b</td> <td>display position in absolute coordinates</td></tr>
<tr> <td>add</td> <td>a</td> <td>added feature(s) to superimpose on the image</td></tr>
<tr> <td>style</td> <td>s</td> <td>stylesheet for additional features</td></tr>
<tr> <td>keystyle</td><td>k</td> <td>where to place the image key</td></tr>
<tr> <td>overview</td><td>&nbsp;</td> <td>force an overview-style display</td></tr>
<tr> <td>flip</td> <td>f</td> <td>flip image left to right</td></tr>
<tr> <td>grid</td> <td>&nbsp;</td> <td>turn grid on (1) or off (0)</td></tr>
<tr> <td>embed</td> <td>&nbsp;</td> <td>generate full HTML for image and imagemap for use in an embedded frame</td></tr>
<tr> <td>format</td> <td>&nbsp;</td> <td>format for the image (use "SVG" for scaleable vector graphics)</td></tr>
<tr> <td>list</td> <td>&nbsp;</td> <td>get certain types of configuration information</td></tr>
<tr> <td>source</td> <td>&nbsp;</td> <td>database name</td></tr>
<p>The arguments are explained in more detail here</p>
<dt><b>name</b> (Alias: <b>q</b>)
<dd>This argument specifies the region of the genome to be displayed. Several
forms are recognized:
<li><i>name=Landmark</i> Display the landmark named "Landmark". Valid landmark
names include chromosomes, contigs, clones, STSs, predicted genes, and any other
landmark that the administrator has designated. Be careful when fetching large
landmarks such as whole chromosomes!
<li><i>name=Landmark:start..end</i> Display the region between <i>start</i> and <i>end</i>
relative to "Landmark".
<li><i>name=Class:Landmark</i> Display "Landmark", restricting to a particular class, such
as "PCR_Product". The list of classes is under the control of the database administrator
and is not yet available through this interface.
<li><i>name=Class:Landmark:start..end</i> As above, but restricted to the designated range.
If you use multiple <b>name</b> options, then this script will generate an overview
image showing the position of each landmark. The alias "q" can be used to
shorten the length of the URL.
<dt><b>type</b> (Aliases: <b>t</b>, <b>track</b>)
<dd>This argument lists the feature types to display. The value of this argument is
a list of track names separated by spaces ("+" characters when URL-escaped). For example:
&lt;img src=";
Multiple <i>type=</i> arguments will be combined to form a single space-delimited list.
The alias "t" can be used to shorten the length of the URL.
If the track name has a space in it, put quotes around the name:
type="microbe tRNA"+NG+WABA+CG+ESTB
<dt><b>width</b> (Alias: <b>w</b>)
<dd>Width of the desired image, in pixels.
<dt><b>options</b> (Alias: <b>o</b>)
<dd>A space-delimited list ("+" characters when URL-escaped) of mnemonic/option
pairs describing how features should be
formatted. Options are integers from 0 to 3, where
0=auto, 1=compact, 2=expanded, 3=expanded and labeled. For example, to specify that
the tRNA and NG tracks should always be expanded and labeled, but that the WABA
track should be compact, use:
The alias "o" can be used to shorten the length of the URL.
<dt><b>add</b> (Alias: <b>a</b>)
<dd>Superimpose one or more additional features on top of the view. Features are specified
as space ("+") delimited lists in the following format:
"Landmark" is the landmark name, "Type" is a descriptive type that will be printed
in the image caption, "Name" is a name for the feature to be printed above it,
and start..end is a comma-delimited list of ranges for discontinuous feature.
Names that contain white space must be quoted, for example "BLAST hit".
Note that this all has to be URL-escaped, so an additional
feature named "Your Sequence", type "Blast Hit", that is located on chromosome III
in a gapped range between 20000 and 22000, will be formatted as:
One or both of the type and name can be omitted. If omitted, type will
default to "Your Features" and the name will default to "Feature XX" where
XX is an integer. This allows for a very simple feature line:
Multiple <i>add=</i> arguments are allowed. The alias "a" can be used to
shorten the length of the URL.
<dd>The style argument can be used to control the rendering of additional features added
with "add". It is a flattened version of the style configuration sections described
in <a href="">this document</a>
For example, if you have added a "Blast Hit" annotation, then you can tell the
renderer to use a red arrow for this glyph in this way:
<dt><b>keystyle</b> (Alias: <b>k</b>)
<dd>Controls the positioning of the track key. One of "right", "left", "between" (default)
or "bottom"
<dd>Ordinarily the image will show the detail panel if the query region corresponds to
a single region, and the overview panel if multiple regions match (or if a region
that is too large to show matches). Setting overview=1 will force the overview
to be shown in all cases.
<dt><b>flip</b> (Alias: <b>f</b>)
<dd>Flip the image left to right. Arguments are 0=don't flip (default), and 1=flip.
<dd>Generate image and a corresponding HTML imagemap in a form suitable for embedding
into a frame.
<dd>Specify the format for the image file. Either "GD" (the default) or
"GD::SVG" for scaleable vector graphics.
<dd>If this argument is present, it will cause the script to dump
out various types of information in plain text form. Currently the two
values for this argument are <i>sources</i>, to dump out the list of
data sources, and <i>types</i>, to dump out the list of configured
types. For <i>list=sources</i>, the script will return a simple
text list of the data source names. For <i>list=types</i>, the
script will return a three-column tab-delimited list giving the
track names and feature types corresponding to the currently-selected
data source. The format is as follows:
Mnemonic &lt;tab&gt; Full description of feature &lt;tab&gt; [default]
The third column contains the word "default" if the track will be shown
by default when no <i>type</i> argument is provided.
<dd>This argument specifies the database for the images. The list of sources
can be found using <i>list=sources</i>.
<dd>The name of a feature to highlight in the format <i>feature_name</i>@<i>color_name</i>".
You may omit "@color", in which case the highlight will default to
yellow. You can specify multiple h_feat arguments in order to
highlight several features with distinct colors.
<dd>The name of a region to highlight in a solid background color, in the
format <i>sequence_name</i>:<i>start</i>..<i>end</i>@<i>color_name</i>".
You may omit "@color", in which case the highlighted region
will default to
lightgrey. You can specify multiple h_region arguments in order to
highlight several regions with distinct colors.
Putting it all together, here's a working (very long) URL:
<pre><a href=";add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1">;add=B0001+pcr+pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..5000;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=transcript2+bgcolor=orange;abs=1</a>
If you wish to associate the image with an imagemap so that clicking
on a feature takes the user to the destination configured in the
gbrowse config file, you may do so by placing the URL in an
&lt;iframe&gt; section and using the <b>embed=1</b> flag:
&lt;iframe src="http://localhost/cgi-bin/gbrowse_img/c_elegans?name=B0001;embed=1" width="100%" height="250"&gt;
&lt;img src="http://localhost/cgi-bin/gbrowse_img/c_elegans?name=B0001"/&gt;
Placing an &lt;img&gt; tag inside the &lt;iframe&gt; tag arranges for
older browsers that don't know about iframes to display the static
image instead. You may need to adjust the width and height attributes
in order to avoid browsers placing scrollbars around the frame.
<h2>KNOWN BUGS</h2>
<p> The cookie that stores the configuration options for plugins does
not transfer from gbrowse to gbrowse_img, so tracks generated by
annotation plugins, such as the Restriction site annotator, will not
display correctly when the image URL is generated on one machine and
then viewed on another. Uploaded files will transfer correctly,
<p>Lincoln Stein <a href=""></a>
Copyright (c) 2002-2004 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
For additional help, see <a href="">The GMOD Project</a> pages.
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