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');
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.
- $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 entended 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.