SYNOPSIS

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

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

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 .wig 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.

METHODS

$loader = Bio::Graphics::Wiggle::Loader->new('/base/directory')

Create a new loader. Specify the base directory in which the loaded .wig files will be created.

$loader->load($fh)

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

$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 properlyl 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 do display the data.

EXTENSIONS

Several extensions to the WIG format "track" declaration are recognized.

transform=<transform>

Specify a transform to be performed on all numeric data within this track prior to loading into the binary wig file. Currently, the following two declarations are recognized:

 transform=logsquared  y' = log(y**2) for y != 0
                       y' = 0         for y == 0
            
 transform=none        y' = y   (no transform - the default)

trim=<trim>

Specify a trimming function to be performed on the data prior to scaling. Currently, the following trim functions are recognized:

 trim=stdev1           trim to plus/minus 1 standard deviation of the mean
 trim=stdev2           trim to plus/minus 2 standard deviations of the mean
 trim=stdevN           trim to plus/minus N standard deviations of the mean
 trim=none             no trimming (the default)

Example entended track declaration:

 track type=wiggle_0 name="example" description="20 degrees, 2 hr"  \
       trim=stdev2 transform=logsquared

SEE ALSO

the Bio::Graphics::Wiggle manpage, the Bio::Graphics::Glyph::wiggle_xyplot manpage, the Bio::Graphics::Glyph::wiggle_density manpage, the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Feature manpage, the Bio::Graphics::FeatureFile manpage

AUTHOR

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2007 Cold Spring Harbor Laboratory

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.