Bio-Graphics

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Changes  view on Meta::CPAN

       of the window is <= that number. For compatibility, a value of "1" is the same as "base level."
     - Fixed display of protein sequence in genes when -draw_protein is true.
     - Fixed display of long deletions in segments glyph base-pair alignments to avoid drop-out of
       sequence from the right end of the alignment following deleted region.
     - Fixed display of insertions in segments glyph base-pair alignments so that the length
       of the deletion is displayed when there is more than one digit of length.
     - Fixed Wiggle loader routine to handle statistics on chromosomes that have a 
       combination of fixed and variable step declarations.

2.03 Fri Mar 26 16:32:02 EDT 2010
     - Bad CPAN upload. Do not use.

2.02 Sun Mar 14 18:44:04 EDT 2010
     - Added a wiggle_whiskers glyph that works nicely with BigWig and
       BigBed data.
     - Fixed processed_transcript (and gene) glyphs so that thin UTRs are more attractive.
     - Fixed the behavior of transcript arrows to be more customizable and not to get
       too large.
     - Segments glyph now shows mismatches when zoomed out and -show_mismatches is true.
     - Added an -indel_color option to segments glyph to show indels in a different color
       from simple nucleotide substitutions.

Changes  view on Meta::CPAN

1.993 Thu Dec  3 06:36:06 EST 2009
      - Fixed issue which caused GD::SVG rendering of xyplot glyph to show scale
      but no values under some circumstances.

1.992 Wed Nov 18 13:06:07 EST 2009
      - Fixed issue in which the connector vanishes when zoomed in to
        the region between two parts (such as the region between two
        exons)

1.991 Mon Nov 16 09:20:18 EST 2009
      - CPAN upload failed due to lack of $VERSION in hybrid_plot. Uploaded again.
1.99 Mon Nov 16 08:15:23 EST 2009  
     - Segments glyph now handles indels for features that have CIGAR strings.
1.982 Wed Aug 26 17:57:43 EDT 2009
     - Fixed DAS stylesheet support so that Ensembl and Dazzle sources both work
       properly.	 
1.981 Wed Aug 19 15:21:31 EDT 2009
     - Peter Ruzanov fixed bug in wiggle_xyplot that caused histogram to go to background
       color under some circumstances.
1.98 Mon Jul  6 09:48:58 EDT 2009
     - Documented -feature_limit in the Panel docs as well as in Glyph.

Changes  view on Meta::CPAN

0.85  Mon Oct  1 16:41:57 EDT 2001  (LS)
	- Changed all instances of stop() to end() so that BioSeqFeatureI is supported
	  correctly.

0.82  Fri Jul 20 10:36:57 EDT 2001  (LS)
	- Removed perl 5.6'isms.
	- Added appropriate documentation to Feature.

0.81  Tue Jun 12 09:30:10 EDT 2001  (LS)
	- Messed up sourceforge upload, so bumping version no
		to clean up.

0.80  Tue Jun 12 09:10:15 EDT 2001  (LS)
	- Basically functional
	- examples in eg/
	- Bio::Graphics::Panel documentation complete,
		other documentation incomplete

0.01  Tue Jun  5 07:26:52 2001  (LS)
	- original version; created by h2xs 1.20 with options

lib/Bio/Graphics/Wiggle/Loader.pm  view on Meta::CPAN

package Bio::Graphics::Wiggle::Loader;

=head1 SYNOPSIS

  my $loader = Bio::Graphics::Wiggle::Loader->new('/base/directory/for/wigfiles','wibfilename');
  my $fh = IO::File->new('uploaded_file.txt');
  $loader->load($fh);

  my $gff3_file   = $loader->featurefile('gff3',$method,$source);
  my $featurefile = $loader->featurefile('featurefile');
  my @features    = $loader->features();

=head1 USAGE

This module loads Bio::Graphics::Wiggle files from source files that
use Jim Kent's "WIG" format:

scripts/frend.pl  view on Meta::CPAN

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')