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();

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.

   METHODS
       $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.

       $loader->load($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 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.

       @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.

       $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.

   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 three declarations are
           recognized:

            transform=logtransform y' = 0          for  y == 0
                                   y' = log(y)     for  y >  0
                                   y' = -log(-y)   for  y <  0

            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 (default)
            trim=stdevN           trim to plus/minus N standard deviations of the mean
            trim=none             no trimming

       Example intended track declaration:

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

SEE ALSO

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

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.