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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:

http://genome.ucsc.edu/google/goldenPath/help/wiggle.html

Several data sets can be grouped together in a single WIG source
file. The load() method accepts the path to a WIG source file, and
will create one or more .wib ("wiggle binary") databases of
quantitative data in the directory indicated when you created the
loader. Call the featurefile() method to return a text file in either
GFF3 or Bio::Graphics::FeatureFile format, suitable for loading into a
gbrowse database.

=head2 METHODS

=over 4

=item $loader = Bio::Graphics::Wiggle::Loader->new('/base/directory' [,'my_data'])

Create a new loader. The first argument specifies the base directory
in which the loaded .wib files will be created. The second argument
specifies the base name for the created .wib files, or "track" if not
specified.

=item $loader->load($fh)

Load the data from a source WIG file opened on a filehandle.

=item $data = $loader->featurefile($type [,$method,$source])

Return the data corresponding to a GFF3 or
Bio::Graphics::FeatureFile. The returned file will have one feature
per WIG track, and a properly formatted "wigfile" attribute that
directs Bio::Graphics to the location of the quantitative data.

$type is one of "gff3" or "featurefile". In the case of "gff3", you
may specify an optional method and source for use in describing each
feature. In the case of "featurefile", the returned file will contain
GBrowse stanzas that describe a reasonable starting format to display
the data.

=item @features = $loader->features

Returns one or more Bio::Graphics::Features objects, which can be used to
create Bio::Graphics tracks with the wiggle_xyplot (and related) glyphs.

=item $loader->allow_sampling(1)

If allow_sampling() is passed a true value, then very large files
(more than 5 MB) will undergo a sampling procedure to find their
minimum and maximum values and standard deviation. Otherwise, file
will be read in its entirety to generate those statistics.