.\" Automatically generated by Pod::Man 4.09 (Pod::Simple 3.35) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. 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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "SYNOPSIS" .IX Header "SYNOPSIS" .Vb 3 \& my $loader = Bio::Graphics::Wiggle::Loader\->new(\*(Aq/base/directory/for/wigfiles\*(Aq,\*(Aqwibfilename\*(Aq); \& my $fh = IO::File\->new(\*(Aquploaded_file.txt\*(Aq); \& $loader\->load($fh); \& \& my $gff3_file = $loader\->featurefile(\*(Aqgff3\*(Aq,$method,$source); \& my $featurefile = $loader\->featurefile(\*(Aqfeaturefile\*(Aq); \& my @features = $loader\->features(); .Ve .SH "USAGE" .IX Header "USAGE" This module loads Bio::Graphics::Wiggle files from source files that use Jim Kent's \*(L"\s-1WIG\*(R"\s0 format: .PP http://genome.ucsc.edu/google/goldenPath/help/wiggle.html .PP Several data sets can be grouped together in a single \s-1WIG\s0 source file. The \fIload()\fR method accepts the path to a \s-1WIG\s0 source file, and will create one or more .wib (\*(L"wiggle binary\*(R") databases of quantitative data in the directory indicated when you created the loader. Call the \fIfeaturefile()\fR method to return a text file in either \&\s-1GFF3\s0 or Bio::Graphics::FeatureFile format, suitable for loading into a gbrowse database. .SS "\s-1METHODS\s0" .IX Subsection "METHODS" .ie n .IP "$loader = Bio::Graphics::Wiggle::Loader\->new('/base/directory' [,'my_data'])" 4 .el .IP "\f(CW$loader\fR = Bio::Graphics::Wiggle::Loader\->new('/base/directory' [,'my_data'])" 4 .IX Item "$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 \*(L"track\*(R" if not specified. .ie n .IP "$loader\->load($fh)" 4 .el .IP "\f(CW$loader\fR\->load($fh)" 4 .IX Item "$loader->load($fh)" Load the data from a source \s-1WIG\s0 file opened on a filehandle. .ie n .IP "$data = $loader\->featurefile($type [,$method,$source])" 4 .el .IP "\f(CW$data\fR = \f(CW$loader\fR\->featurefile($type [,$method,$source])" 4 .IX Item "$data = $loader->featurefile($type [,$method,$source])" Return the data corresponding to a \s-1GFF3\s0 or Bio::Graphics::FeatureFile. The returned file will have one feature per \s-1WIG\s0 track, and a properly formatted \*(L"wigfile\*(R" attribute that directs Bio::Graphics to the location of the quantitative data. .Sp \&\f(CW$type\fR is one of \*(L"gff3\*(R" or \*(L"featurefile\*(R". In the case of \*(L"gff3\*(R", you may specify an optional method and source for use in describing each feature. In the case of \*(L"featurefile\*(R", the returned file will contain GBrowse stanzas that describe a reasonable starting format to display the data. .ie n .IP "@features = $loader\->features" 4 .el .IP "\f(CW@features\fR = \f(CW$loader\fR\->features" 4 .IX Item "@features = $loader->features" Returns one or more Bio::Graphics::Features objects, which can be used to create Bio::Graphics tracks with the wiggle_xyplot (and related) glyphs. .ie n .IP "$loader\->\fIallow_sampling\fR\|(1)" 4 .el .IP "\f(CW$loader\fR\->\fIallow_sampling\fR\|(1)" 4 .IX Item "$loader->allow_sampling" If \fIallow_sampling()\fR is passed a true value, then very large files (more than 5 \s-1MB\s0) 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. .SS "\s-1EXTENSIONS\s0" .IX Subsection "EXTENSIONS" Several extensions to the \s-1WIG\s0 format \*(L"track\*(R" declaration are recognized. .IP "transform=" 4 .IX Item "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: .Sp .Vb 3 \& transform=logtransform y\*(Aq = 0 for y == 0 \& y\*(Aq = log(y) for y > 0 \& y\*(Aq = \-log(\-y) for y < 0 \& \& \& transform=logsquared y\*(Aq = log(y**2) for y != 0 \& y\*(Aq = 0 for y == 0 \& \& transform=none y\*(Aq = y (no transform \- the default) .Ve .IP "trim=" 4 .IX Item "trim=" Specify a trimming function to be performed on the data prior to scaling. Currently, the following trim functions are recognized: .Sp .Vb 4 \& 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 .Ve .PP Example entended track declaration: .PP .Vb 2 \& track type=wiggle_0 name="example" description="20 degrees, 2 hr" \e \& trim=stdev2 transform=logsquared .Ve .SH "SEE ALSO" .IX Header "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 .SH "AUTHOR" .IX Header "AUTHOR" Lincoln Stein . .PP Copyright (c) 2007 Cold Spring Harbor Laboratory .PP This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the \s-1GPL\s0 (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to \s-1LICENSE\s0 for the full license text. In addition, please see \s-1DISCLAIMER\s0.txt for disclaimers of warranty.