view release on metacpan or  search on metacpan

scripts/frend.pl  view on Meta::CPAN

=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;