#!/usr/bin/perl -w
=head1 NAME
frend.pl -- Render a Bio::Graphics Feature File on the web
=head1 SYNOPSIS
http://your.host.com/cgi-bin/frend.pl
=head1 DESCRIPTION
The frend.pl script is a thin front end around the Bio::Graphics
module. It accepts a list of files containing sequence (protein,
nucleotide) feature coordinates from the file(s) listed on the command
line or on standard input, renders them, and produces a PNG file on
standard output.
=head1 INSTALLATION
Copy this script into your web site's cgi-bin directory. Name it
whatever you want.
=head1 Feature Files Format
This script accepts and processes sequence annotations in a simple
tab-delimited format or in GFF format.
The feature file format has a configuration section and a data
section. The configuration section sets up the size and overall
properties of the image, and the data section gives the feature
data itself.
=head2 Configuration Section
If not provided, this scripts generates a reasonable default
configuration section for you, so you do not need to provide a
configuration section to get a reasonable image. However, to tune the
appearance of the image, you will probably want to tweak the
configuration. Here is an excerpt from the configuration section:
# example file
[general]
bases = -1000..21000
height = 12
[EST]
glyph = segments
bgcolor= yellow
connector = solid
height = 5
[FGENES]
glyph = transcript2
bgcolor = green
description = 1
The configuration section is divided into a set of sections, each one
labeled with a [section title]. The [general] section specifies global
options for the entire image. Other sections apply to particular
feature types. In the example above, the configuration in the [EST]
section applies to features labeled as ESTs, while the configuration
in the [FGENES] section applies to features labeled as predictions
from the FGENES gene prediction program.
Inside each section is a series of name=value pairs, where the name is
the name of an option to set. You can put whitespace around the = sign
to make it more readable, or even use a colon (:) if you prefer. The
following option names are recognized:
Option Value Example
------ ----- -------
bases Min & max of the sequence range (bp) 1200..60000
width width of the image (pixels) 600
height Height of each graphical element (pixels) 10
glyph Style of each graphical element (see below) transcript
fgcolor Foreground color of each element yellow
bgcolor Background color of each element blue
linewidth Width of lines 3
label Print the feature's name 1
description Whether to print the feature's description 0
bump Elements are not allowed to collide 1
ticks Print tick marks on arrows 1
connector Type of group connector (dashed, hat or solid) dashed
The "bases" and "width" options are only relevant in the [general]
section. They are overridden by the like-named command-line options.
The remainder of the options can be located in any section, but if
present in the [general] section will set defaults for the others.
Colors are English-language color names or Web-style #RRGGBB colors
(see a book on HTML for an explanation). True/false values are 1 for
true, and 0 for false. Numeric ranges can be expressed in start..end
fashion with two dots, or as start-end with a hyphen.
The "glyph" option controls how the features are rendered. The
following glyphs are implemented:
Name Description
---- -----------
box A filled rectangle, nondirectional.
ellipse An oval.
arrow An arrow; can be unidirectional or
bidirectional. It is also capable of displaying
a scale with major and minor tickmarks, and can
be oriented horizontally or vertically.
segments A set of filled rectangles connected by solid
lines. Used for interrupted features, such as
gapped alignments and exon groups.
transcript Similar to segments, but the connecting line is
a "hat" shape, and the direction of
transcription is indicated by a small arrow.
transcript2 Similar to transcript, but the direction of
transcription is indicated by a terminal segment
in the shape of an arrow.
primers Two inward pointing arrows connected by a line. Used for STSs.
The bump option is the most important option for controlling the look
of the image. If set to false (the number 0), then the features are
allowed to overlap. If set to true (the number 1), then the features
will move vertically to avoid colliding. If not specified, bump is
turned on if the number of any given type of sequence feature is
greater than 50.
=head2 Data Section
The data section can follow or proceed the configuration section. The
two sections can also be intermixed. The data section is a tab or
whitespace-delimited file which you can export from a spreadsheet
application or word processor file (be sure to save as text only!)
Here is an example data section:
Cosmid B0511 . 516-619
Cosmid B0511 . 3185-3294
Cosmid B0511 . 10946-11208
Cosmid B0511 . 13126-13511
Cosmid B0511 . 66-208
Cosmid B0511 . 6354-6499
Cosmid B0511 . 13955-14115
EST yk595e6.5 + 3187-3294
EST yk846e07.3 - 11015-11208
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
EST yk53c10.5 + 16032-16105
SwissProt PECANEX + 13153-13656 Swedish fish
FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
Each line of the file contains five columns. The columns are:
Column # Description
-------- -----------
1 feature type
2 feature name
3 strand
4 coordinates
5 description
=over 4
=item Feature type
The feature type should correspond to one of the [feature type]
headings in the configuration section. If it doesn't, the [general]
options will be applied to the feature when rendering it. The feature
name is a name for the feature. Use a "." or "-" if this is not
relevant. If the name contains whitespace, put single or double quotes
("") around the name.
=item Strand
The strand indicates which strand the feature is on. It is one of "+"
for the forward strand, "-" for the reverse strand, or "." for
features that are not stranded.
=item Coordinates
The coordinates column is a set of one or more ranges that the feature
occupies. Ranges are written using ".." as in start..stop, or with
hyphens, as in start-stop. For features that are composed of multiple
ranges &em; for example transcripts that have multiple exons &em; you
can either put the ranges on the same line separated by commas or
spaces, or put the ranges on individual lines and just use the same
feature name and type to group them. In the example above, the Cosmid
B0511 features use the individual line style, while the FGENESH
features use the all-ranges-on-one-line style.
=item Description
The last column contains some descriptive text. If the description
option is set to true, this text will be printed underneath the
feature in the rendering.
=back
Finally, it is possible to group related features together. An example
is the ESTs yk53c10.5 and yk53c10.3, which are related by being reads
from the two ends of the clone yk53c10. To indicate this relationship,
generate a section that looks like this:
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
The group is indicated by a line that contains just two columns
containing the feature type and a unique name for the group. Follow
this line with all the features that form the group, but leave the
first column (the feature type) blank. The group will be rendered by
drawing a dashed line between all the members of the group. You can
change this by specifying a different connector option in the
configuration section for this feature type.
=head1 BUGS
Please report them to the author.
=head1 SEE ALSO
L<Bio::Graphics>, L<feature_draw.pl>
=head1 AUTHOR
Lincoln Stein, lstein@cshl.org
=cut
use strict;
use Bio::Graphics::Panel;
use Bio::Graphics::Feature;
use Bio::Graphics::FeatureFile;
use CGI qw(:standard);
use CGI::Carp;
use File::Temp ':mktemp';
use File::Spec;
use File::Basename 'basename';
use File::Path 'mkpath';
use vars '@COLORS';
use constant WIDTH => 600; # default width
use constant BUMP_THRESHOLD => 50; # if more than this # of features, will stop bumping
@COLORS = qw(cyan blue red yellow green wheat turquoise orange); # default colors
if (param('cat')) {
catfile(param('cat'));
exit 0;
}
print header,start_html('Sequence Feature Renderer');
print h1('Sequence Feature Renderer');
print p('This is a front end to the Bio::Graphics package, a part of the',
a({-href=>'http://www.bioperl.org'},'BioPerl library.'),
'Cut and paste your sequence annotation data into the text field below, or upload it using the',
'upload button.',
'The format of the annotation data is explained',a({-href=>'#format'},'below.'));
my $self = url(-relative=>1);
print h3('Instant examples'),
p('For the impatient, you can paste in an',
b(a({-href=>"$self?Paste+Example+1"},'example file.')));
read_file() if param('file');
my $example = param('Example 1')
? test_data(0)
: param('Example 2')
? test_data(1)
: '';
param(text => $example) if length $example;
render() if param('text') || param('file') =~ /\w/;
print start_multipart_form(),
table({-border=>0,-width=>300,-cellspacing=>0,-cellpadding=>0},
TR({-class=>'resultsbody'},
td({-colspan=>1},
'Cut and Paste the annotation file...'
),
td({-colspan=>2},
'Image width: ',
popup_menu(-name=>'width',-values=>[480,640,800,1024,1280,1600],-default=>800)
),
TR({-class=>'resultsbody'},
td({-colspan=>3},
pre(
textarea(-name=>'text',-value=>$example,
-cols=>80,-rows=>10,-wrap=>'off',-override=>length $example || param('Clear'))
)
)
)
),
TR({-class=>'resultsbody'},
td({-colspan=>1},'Upload it... ',filefield(-name=>'file',-size=>30)),
td({-align=>'left',-colspan=>2},
'Or paste one of the example files...',
submit('Example 1'),
submit('Example 2'),
submit('Clear'),
)
),
TR({-class=>'resultstitle'},
td({-align=>'left',-colspan=>3},
"Press",b('Render'),'when ready...',
b(submit('Render...'))
),
)),
end_form;
print_format();
print hr(),a({-href=>'http://www.bioperl.org'},'www.bioperl.org'),end_html();
exit 0;
sub read_file {
my $text;
my $fh = param('file') or return;
$text .= $_ while <$fh>;
param(text => $text);
}
sub render {
my $text = shift;
my $color = 0; # position in color cycle
$text ||= param('text');
my $data = $text ? Bio::Graphics::FeatureFile->new(-text => $text)
: Bio::Graphics::FeatureFile->new(-file => param('file'));
unless ($data->min < $data->max) {
AceError("This doesn't look like a valid annotation file. No annotations found.");
exit 0;
}
# adjust the width if requested
$data->setting(general => 'width',param('width')) if param('width');
# render the panel
my $panel = $data->new_panel;
$data->render($panel);
# we create the file and write it out
my $gd = $panel->gd;
my $suffix = $gd->can('gif') ? '.gif' : '.png';
my $dir = tmpdir();
mkpath($dir) unless -e $dir;
my($fh,$filename) = mkstemps(tmpfile('XXXXXXXX'),$suffix);
print $fh ($gd->can('gif') ? $gd->gif : $gd->png);
close $fh;
# now we send the link to the user
my $self = url(-relative=>1);
my $base = basename($filename);
my $url = "$self/features$suffix?cat=$base";
my ($w,$h) = $gd->getBounds;
print hr(),h2('Rendering');
print a({-name=>'rendering'},
img({-src=>$url,-alt=>'Right-click and "Save As..." to save this image',
-border=>0,-width=>$w,-height=>$h})
);
}
sub tmpdir {
return File::Spec->catfile(File::Spec->tmpdir,'frend');
}
sub tmpfile {
return File::Spec->catfile(tmpdir(),shift);
}
sub catfile {
my $file = shift;
my $path = tmpfile($file);
print header($path =~ /\.gif$/ ? 'image/gif' : 'image/png');
open F,$path or die "Couldn't open $file for reading: $!";
print while <F>;
close F;
unlink $path;
}
sub print_format {
print hr();
print a({-name=>'format'},h2('Annotation file format'));
print <<END;
<p>
The annotation file format has a configuration section and a data section. The configuration section
sets up the size and overall properties of the image, and the data section gives the annotation data
itself.
<p>
<h3>Configuration Section</h3>
<p>
If not provided, this page generates a reasonable default configuration section for you, so you
do not need to provide a configuration section to get a reasonable image. However, to tune the
appearance of the image, you will probably want to tweak the configuration. Here is an excerpt
from the configuration section:
<blockquote>
<pre>
# example file
[general]
bases = -1000..21000
height = 12
[EST]
glyph = segments
bgcolor= yellow
connector = solid
height = 5
[FGENES]
glyph = transcript2
bgcolor = green
description = 1
</pre>
</blockquote>
<p>
The configuration section is divided into a set of sections, each one labeled with a [section title].
The [general] section specifies global options for the entire image. Other sections apply to particular
feature types. In the example above, the configuration in the [EST] section applies to features labeled
as ESTs, while the configuration in the [FGENES] section applies to features labeled as predictions from
the FGENES gene prediction program.
<p>
Inside each section is a series of <i>name</i>=<i>value</i> pairs, where the name is the name of
an option to set. You can put whitespace around the = sign to make it more readable, or even use
a colon (:) if you prefer. The following option names are recognized:
<p>
<table border="1">
<tr>
<th>Option</th><th>Value</th><th>Example</th>
</tr>
<tr>
<th>bases</th><td>Min & max of the sequence range (bp)</td><td>1200..60000</td>
</tr>
<tr>
<th>width</th><td>width of the image (pixels)</td> <td>600</td>
</tr>
<tr>
<th>height</th><td>Height of each graphical element (pixels)</td><td>10</td>
</tr>
<tr>
<th>glyph</th><td>Style of each graphical element (see below)</td><td>transcript</td>
</tr>
<tr>
<th>fgcolor</th> <td>Foreground color of each element</td> <td>yellow</td>
</tr>
<tr>
<th>bgcolor</th> <td>Background color of each element</td> <td>blue</td>
</tr>
<tr>
<th>linewidth</th> <td>Width of lines</td> <td>3</td>
</tr>
<tr>
<th>label</th> <td>Print the feature's name</td> <td>1</td>
</tr>
<tr>
<th>description</th> <td>Whether to print the feature's description </td> <td>0</td>
</tr>
<tr>
<th>bump</th> <td>Elements are not allowed to collide</td> <td>1</td>
</tr>
<tr>
<th>ticks</th> <td>Print tick marks on arrows</td> <td>1</td>
</tr>
<tr>
<th>connector</th> <td>Type of group connector (dashed, hat or solid)</td> <td>dashed</td>
</tr>
</table>
<p>
The "bases" and "width" options are only relevant in the [general]
section. The rest can be located in any section, but if present in
the [general] section will set defaults for the others.
<p>
Colors are English-language color names or Web-style #RRGGBB colors
(see a book on HTML for an explanation). True/false values are 1 for
true, and 0 for false. Numeric ranges can be expressed in
<i>start</i>..<i>end</i> fashion with two dots, or as
<i>start</i>-<i>end</i> with a hyphen.
<p>
The "glyph" option controls how the features are rendered. The
following glyphs are implemented:
<p>
<table border="1">
<tr><th>Name</th><th>Description</th></tr>
<tr>
<th>
box
</th>
<td>A filled rectangle, nondirectional.</td>
</tr>
<tr>
<th>ellipse</th><td>An oval.</td>
</tr>
<tr>
<th>arrow</th>
<td> An arrow; can be unidirectional or bidirectional.
It is also capable of displaying a scale with
major and minor tickmarks, and can be oriented
horizontally or vertically.
</td>
</tr>
<tr>
<th>segments</th>
<td> A set of filled rectangles connected by solid lines.
Used for interrupted features, such as gapped
alignments.
</td>
</tr>
<tr>
<th>transcript</th>
<td>
Similar to segments, but the connecting line is
a "hat" shape, and the direction of transcription
is indicated by a small arrow.
</td>
</tr>
<tr>
<th>
transcript2</th>
<td> Similar to transcript, but the direction of
transcription is indicated by a terminal segment
in the shape of an arrow.
</td>
</tr>
<tr>
<th>
primers
</th>
<td> Two inward pointing arrows connected by a line.
Used for STSs.
</td>
</tr>
</table>
<p>
The <b>bump</b> option is the most important option for controlling the look
of the image. If set to false (the number 0), then the features are allowed
to overlap. If set to true (the number 1), then the features will move
vertically to avoid colliding. If not specified, bump is turned on
if the number of any given type of sequence feature is greater than
${\BUMP_THRESHOLD}.
<h3>Data Section</h3>
<p>
The data section can follow or proceed the configuration section. The two sections
can also be intermixed. The data section is a tab or whitespace-delimited file which you can
export from a spreadsheet application or word processor file (be sure to save as text only!)
<p>
Here is an example data section:
<p>
<blockquote>
<pre>
Cosmid B0511 . 516-619
Cosmid B0511 . 3185-3294
Cosmid B0511 . 10946-11208
Cosmid B0511 . 13126-13511
Cosmid B0511 . 66-208
Cosmid B0511 . 6354-6499
Cosmid B0511 . 13955-14115
EST yk595e6.5 + 3187-3294
EST yk846e07.3 - 11015-11208
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
EST yk53c10.5 + 16032-16105
SwissProt PECANEX + 13153-13656 Swedish fish
FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
</pre>
</blockquote>
<p>
Each line of the file contains five columns. The columns are:
<p>
<table border="1">
<tr><th>Column #</th><th>Column Description</th></tr>
<tr><td align="right">1</td><td>feature type</td></tr>
<tr><td align="right">2</td><td>feature name</td></tr>
<tr><td align="right">3</td><td>strand</td></tr>
<tr><td align="right">4</td><td>coordinates</td></tr>
<tr><td align="right">5</td><td>description</td></tr>
</table>
<p>
The <b>feature type</b> should correspond to one of the [feature type] headings
in the configuration section. If it doesn't, the [general] options will
be applied to the feature when rendering it. The <b>feature name</b> is a
name for the feature. Use a "." or "-" if this is not relevant. If
the name contains whitespace, put single or double quotes ("") around
the name.
<p>
The <b>strand</b>
indicates which strand the feature is on. It is one of "+" for the
forward strand, "-" for the reverse strand, or "." for features that are not
stranded.
<p>
The <b>coordinates</b> column is a set of one or more ranges that the
feature occupies. Ranges are written using ".." as in <i>start</i>..<i>stop</i>,
or with hyphens, as in <i>start</i>-<i>stop</i>. For features that are composed
of multiple ranges &em; for example transcripts that have multiple exons &em;
you can either put the ranges on the same line separated by commas or spaces,
or put the ranges on individual lines and just use the same feature name and
type to group them. In the example above, the Cosmid B0511 features use
the individual line style, while the FGENESH features use the all-ranges-on-one-line
style.
<p>
The last column contains some descriptive text. If the <b>description</b> option
is set to true, this text will be printed underneath the feature in the rendering.
<p>
Finally, it is possible to group related features together. An example is
the ESTs yk53c10.5 and yk53c10.3, which are related by being reads from
the two ends of the clone yk53c10. To indicate this relationship, generate
a section that looks like this:
<p>
<blockquote>
<pre>
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
</pre>
</blockquote>
<p>
The group is indicated by a line that contains just two columns
containing the feature type and a unique name for the group.
Follow this line with all
the features that form the group, but leave the first column
(the feature type) blank. The group will be rendered by
drawing a dashed line between all the members of the group.
You can change this by specifying a different <b>connector</b>
option in the configuration section for this feature type.
END
;
}
sub test_data {
my $config = shift;
my $header = <<'END';
[general]
bases = -1000..21000
height = 12
reference = B0511
[Cosmid]
glyph = segments
fgcolor = blue
key = C. elegans conserved regions
[EST]
glyph = segments
bgcolor= yellow
connector = solid
height = 5
[FGENESH]
glyph = transcript2
bgcolor = green
description = 1
[SwissProt]
glyph = arrow
base = 1
linewidth = 2
fgcolor = red
description = 1
[P-element]
glyph = triangle
orient = S
bgcolor = red
fgcolor = white
label = 1
point = 1
END
;
my $data =<<'END';
Cosmid B0511 516-619
Cosmid B0511 3185-3294
Cosmid B0511 10946-11208
Cosmid B0511 13126-13511
Cosmid B0511 11394-11539
Cosmid B0511 14383-14490
Cosmid B0511 15569-15755
Cosmid B0511 18879-19178
Cosmid B0511 15850-16110
Cosmid B0511 66-208
Cosmid B0511 6354-6499
Cosmid B0511 13955-14115
Cosmid B0511 7985-8042
Cosmid B0511 11916-12046
P-element "" 500-500
P-element MrQ 700-700
P-element MrR 10000-10000
EST yk260e10.5 15569-15724
EST yk672a12.5 537-618,3187-3294
EST yk595e6.5 552-618
EST yk595e6.5 3187-3294
EST yk846e07.3 11015-11208
EST yk53c10
yk53c10.3 12876-13577,13882-14121,14169-14535
yk53c10.5 18892-19154,15853-16219
SwissProt "PECANEX Protein" 5513-16656 "From SwissProt"
FGENESH "Predicted gene 1" -1200--500,518-616,661-735,3187-3365,3436-3846 Pfam domain
FGENESH "Predicted gene 2" 5513-6497,7968-8136,8278-8383,8651-8839,9462-9515,10032-10705,10949-11340,11387-11524,11765-12067,12876-13577,13882-14121,14169-14535,15006-15209,15259-15462,15513-15753,15853-16219 Mysterious
FGENESH "Predicted gene 3" 16626-17396,17451-17597
FGENESH "Predicted gene 4" 18459-18722,18882-19176,19221-19513,19572-30000 "Transmembrane protein"
END
return $config ? $header . $data : $data;
}
__END__